Contacts of the helix formed by residues 93 - 114 (chain A) in PDB entry 4IKV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ALA* 2.7 27.3 + - - +
91A VAL 3.8 0.6 - - - -
92A PHE* 1.3 82.6 - - - +
94A THR* 1.3 63.5 + - - -
95A SER 3.5 2.5 - - - -
97A ALA* 3.2 15.9 + - - +
215A GLY 3.8 2.9 - - - -
217A TYR 3.3 25.1 - - - -
218A VAL* 4.1 2.6 - - - +
219A PRO* 4.4 2.5 - - - -
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Residues in contact with THR 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA* 4.1 11.0 - - + -
89A ASP* 6.1 0.4 - - - -
93A GLY* 1.3 72.7 - - - -
95A SER* 1.3 58.5 + - - +
97A ALA* 3.3 2.9 + - - +
98A VAL* 2.9 34.3 + - - +
138A ASN* 3.7 32.9 - - - +
141A SER* 3.9 22.4 - - - +
142A ILE* 3.4 12.8 + - - +
215A GLY* 3.0 26.6 + - - -
217A TYR 4.6 0.2 + - - -
219A PRO* 5.6 8.2 - - + +
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Residues in contact with SER 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR* 1.3 75.1 + - - +
96A ARG* 1.3 61.5 + - - +
98A VAL 3.3 1.4 + - - -
99A PHE* 3.1 21.8 + - - +
142A ILE* 3.7 12.2 - - - +
203A PHE* 3.6 22.2 - - - -
207A ARG* 3.9 18.8 + - - +
211A LEU* 5.5 2.6 - - - +
214A ALA 3.9 8.8 + - - -
215A GLY* 2.8 30.6 + - - -
216A THR* 4.2 10.7 - - - +
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Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.6 29.2 - - + +
93A GLY 3.8 1.8 + - - -
94A THR 3.4 0.2 - - - -
95A SER* 1.3 76.6 - - - +
97A ALA* 1.3 64.9 + - - +
99A PHE* 3.3 7.2 + - + +
100A TYR* 2.9 49.5 + - + +
207A ARG* 4.9 9.2 - - - +
215A GLY 4.3 0.6 + - - -
216A THR* 6.0 4.3 - - - +
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA* 3.9 8.3 - - + -
92A PHE* 4.1 11.1 - - + +
93A GLY 3.2 19.0 + - - +
94A THR 3.3 5.1 + - - +
96A ARG* 1.3 76.0 - - - +
98A VAL* 1.3 57.2 + - - +
100A TYR* 5.0 1.1 - - - -
101A GLY* 2.9 28.9 + - - -
134A LEU* 3.4 37.4 - - + +
138A ASN* 3.6 14.1 - - - +
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A THR* 4.3 13.2 - - + -
94A THR 2.9 20.5 + - - +
95A SER 3.7 4.9 - - - +
97A ALA* 1.3 78.2 - - - +
99A PHE* 1.3 56.6 + - - +
102A GLY* 2.9 25.3 + - - -
135A LEU* 3.6 33.4 - - + +
138A ASN* 4.3 2.5 - - + -
139A VAL* 3.8 38.6 - - + +
142A ILE* 3.9 8.3 - - + -
200A LEU* 5.0 1.6 - - - +
203A PHE* 3.9 25.6 - - + -
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Residues in contact with PHE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A SER 3.1 14.1 + - - +
96A ARG* 3.7 9.0 - - + +
98A VAL* 1.3 74.7 - - - +
100A TYR* 1.3 90.9 + + - +
102A GLY* 3.2 2.3 + - - -
103A LEU* 3.1 55.2 + - + +
200A LEU* 3.9 12.0 - - + +
203A PHE* 4.1 9.6 - + + -
204A VAL* 3.5 33.7 - - + -
207A ARG* 3.8 23.8 - - - +
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Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 4.7 29.2 - + + -
96A ARG* 2.9 43.9 + - + +
97A ALA* 4.3 1.6 - - - +
99A PHE* 1.3 97.6 - + - +
101A GLY* 1.3 63.0 + - - +
103A LEU* 3.2 16.3 + - + +
104A LEU* 3.1 30.2 + - + +
134A LEU* 4.6 11.4 - - + -
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Residues in contact with GLY 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ALA 2.9 19.1 + - - -
98A VAL 3.9 0.4 - - - -
100A TYR* 1.3 77.0 - - - +
102A GLY* 1.3 62.0 + - - +
104A LEU 3.2 1.6 + - - -
105A ILE* 3.0 30.1 + - - +
131A GLY* 3.3 29.9 - - - -
134A LEU* 3.9 7.0 - - - +
135A LEU* 4.4 2.0 - - - -
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Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A VAL 2.9 21.2 + - - -
99A PHE 3.2 1.5 + - - -
101A GLY* 1.3 73.9 - - - +
103A LEU* 1.3 57.2 + - - +
105A ILE* 3.4 4.5 + - - +
106A MET* 2.9 30.8 + - - +
135A LEU* 3.9 14.4 - - - +
196A MET* 3.8 14.5 - - - +
200A LEU* 3.6 13.3 - - - +
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 3.1 53.3 + - + +
100A TYR* 3.2 20.2 + - + +
102A GLY* 1.3 76.2 - - - +
104A LEU* 1.3 58.0 + - + +
106A MET* 3.4 15.8 + - + +
107A ALA* 3.0 27.5 + - - +
200A LEU* 3.6 21.5 - - + +
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 3.1 18.3 + - + +
101A GLY 3.6 4.7 - - - +
103A LEU* 1.3 73.5 - - + +
105A ILE* 1.3 60.7 + - - +
107A ALA* 3.3 5.2 + - + +
108A GLY 2.9 23.2 + - - -
127A LEU* 3.4 48.0 - - + +
130A LEU* 4.4 12.8 - - + -
131A GLY* 3.7 11.7 - - - +
134A LEU* 4.1 23.3 - - + -
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 3.9 26.7 - - + +
38A SER* 5.5 0.7 - - - -
39A TYR* 6.4 1.6 - - + -
101A GLY 3.0 21.5 + - - +
102A GLY* 3.7 4.7 - - - +
104A LEU* 1.3 72.0 - - - +
106A MET* 1.3 67.9 + - - +
108A GLY* 3.1 10.6 + - - -
109A HIS* 3.1 42.0 + - + +
127A LEU 4.5 0.4 - - - -
128A ILE* 3.9 16.0 - - + +
131A GLY* 3.6 4.5 - - - +
132A THR* 3.6 42.8 - - - +
135A LEU* 4.0 12.3 - - + -
196A MET* 3.8 15.0 - - + -
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Residues in contact with MET 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLY 2.9 18.7 + - - +
103A LEU* 3.7 15.3 - - + +
105A ILE* 1.3 77.1 - - - +
107A ALA* 1.3 63.5 + - + +
109A HIS* 3.2 6.4 + - - +
110A ILE* 3.0 48.5 + - + +
193A ALA 3.9 18.2 - - - +
196A MET* 3.8 12.3 - - + +
197A PHE* 3.9 39.7 - - + +
200A LEU* 4.0 15.7 - - + -
606A OLA 4.8 4.3 - - + -
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU 3.0 13.8 + - - +
104A LEU* 3.5 12.8 - - + +
106A MET* 1.3 77.5 - - + +
108A GLY* 1.3 57.1 + - - +
110A ILE* 3.3 13.2 + - - +
111A ALA* 3.0 28.8 + - - +
127A LEU* 3.9 18.4 - - + +
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Residues in contact with GLY 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LEU 2.9 10.9 + - - -
105A ILE 3.1 5.1 + - - -
107A ALA* 1.3 76.6 - - - +
109A HIS* 1.3 60.8 + - - +
111A ALA* 3.4 7.1 + - - +
112A LEU 3.6 1.6 + - - -
124A SER* 2.9 32.5 + - - -
127A LEU* 3.8 22.6 - - - +
128A ILE* 3.9 11.4 - - - -
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Residues in contact with HIS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A SER* 3.3 46.6 - - - -
39A TYR* 4.3 2.7 + - - -
42A MET* 3.6 23.3 - - + +
105A ILE* 3.1 44.2 + - + +
106A MET 3.7 2.7 - - - +
108A GLY* 1.3 73.5 - - - +
110A ILE* 1.3 66.0 + - - +
112A LEU* 3.1 9.6 + - - +
113A ALA* 3.0 21.1 + - - +
124A SER* 5.0 0.2 - - - -
128A ILE* 3.8 15.5 - - + +
189A PHE* 4.0 6.6 + - - +
192A ALA* 3.7 12.1 - - + +
193A ALA* 3.6 28.3 - - + +
196A MET* 4.3 5.8 - - + -
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Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A MET* 3.0 43.6 + - + +
107A ALA* 3.5 11.7 - - - +
109A HIS* 1.3 75.5 - - - +
111A ALA* 1.3 64.6 + - - +
113A ALA* 3.0 17.6 + - - +
114A ILE* 3.1 30.6 + - + +
193A ALA* 4.1 3.8 - - + -
606A OLA 3.8 36.1 - - + -
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ALA 3.0 12.9 + - - +
108A GLY* 3.4 12.3 - - - +
109A HIS 3.2 0.2 - - - -
110A ILE* 1.3 78.4 - - - +
112A LEU* 1.3 59.7 + - - +
114A ILE* 3.7 23.8 - - - +
120A ALA* 3.6 27.7 - - + +
123A VAL* 4.5 12.3 - - + -
124A SER* 4.1 17.7 - - - +
127A LEU* 4.9 1.1 - - + -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A MET* 4.1 12.1 - - + -
46A LEU* 3.8 14.4 - - + -
49A TYR* 4.0 25.1 - - + +
108A GLY 3.6 1.7 + - - +
109A HIS* 3.1 9.6 + - - +
111A ALA* 1.3 75.4 - - - +
113A ALA* 1.3 55.3 + - - +
114A ILE 3.3 3.4 - - - -
117A GLY 5.7 0.2 - - - +
120A ALA* 4.3 4.5 - - + +
121A LEU* 4.1 21.5 - - + +
124A SER* 3.3 33.0 - - - +
128A ILE* 5.4 0.7 - - + -
186A HIS* 2.7 34.1 + - - -
189A PHE* 3.6 46.3 - - + -
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A HIS 3.0 11.0 + - - +
110A ILE* 3.0 12.9 + - - +
112A LEU* 1.3 79.1 - - - +
114A ILE* 1.3 61.6 + - - +
115A PRO* 4.0 2.3 - - - +
186A HIS* 3.3 28.1 - - - +
189A PHE* 4.0 1.6 - - - -
190A GLY* 3.6 30.5 - - - +
193A ALA* 5.1 0.4 - - + -
606A OLA 4.3 24.0 - - + +
607A OLA 4.4 5.9 - - + +
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Residues in contact with ILE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 3.4 28.3 - - + +
111A ALA* 3.7 21.4 - - - +
112A LEU 3.5 3.8 - - - +
113A ALA* 1.3 80.1 - - - +
115A PRO* 1.3 83.6 - - + +
116A GLY* 3.3 3.6 + - - -
120A ALA* 5.9 1.1 - - + -
186A HIS* 3.4 11.6 + - - -
606A OLA 3.8 26.5 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il