Contacts of the helix formed by residues 102 - 119 (chain A) in PDB entry 4IQJ
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 ASP 102 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LYS* 1.3 93.3 + - + +
103A PHE* 1.3 58.4 + - - +
104A THR* 2.9 42.4 + - - -
105A GLY* 2.8 18.0 + - - -
106A TYR 3.0 9.2 + - - -
138A GLY* 4.1 6.8 + - - -
282A ASP* 3.4 14.4 - - + +
283A VAL* 3.8 10.6 - - - +
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Residues in contact with PHE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASP* 1.3 75.6 - - - +
104A THR* 1.3 61.6 + - - +
106A TYR* 3.2 28.2 + + + +
107A GLN* 3.0 49.9 + - + +
282A ASP 4.1 4.9 + - - -
283A VAL* 4.5 4.4 - - + +
284A ASP 3.3 30.5 - - - +
285A LEU* 4.4 2.2 - - + -
286A PRO* 3.9 21.8 - - + -
294A ARG* 5.5 5.8 - - - -
589A LEU* 3.8 23.8 - - + -
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Residues in contact with THR 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASP* 2.9 16.9 + - - -
103A PHE* 1.3 75.8 - - - +
105A GLY* 1.3 56.1 + - - +
107A GLN* 3.3 16.5 + - - +
108A ASN* 3.0 34.0 + - - +
137A GLN* 4.0 37.2 - - + +
138A GLY* 5.2 0.9 - - - -
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Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ALA* 4.2 4.9 - - - -
101A LYS 4.6 0.2 - - - -
102A ASP* 2.8 12.6 + - - -
104A THR* 1.3 78.1 - - - +
106A TYR* 1.3 56.8 + - - -
108A ASN* 3.4 0.6 + - - -
109A LEU* 2.9 25.6 + - - +
137A GLN 3.9 4.6 + - - -
138A GLY* 3.2 30.9 + - - -
139A LEU* 3.3 14.2 - - - +
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Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 4.9 2.2 - - + -
54A VAL* 4.8 0.2 - - - +
69A ILE* 3.9 28.9 - - + -
100A ALA* 4.1 6.8 - - + +
102A ASP 3.0 5.7 + - - -
103A PHE* 3.2 28.5 + + - +
105A GLY* 1.3 71.9 - - - +
107A GLN* 1.3 64.5 + - + +
109A LEU* 3.3 4.7 + - - +
110A VAL* 3.0 47.7 + - + +
283A VAL* 3.8 20.2 - - + -
285A LEU* 3.4 33.0 - - + +
286A PRO* 5.7 0.2 - - + -
589A LEU* 3.0 38.9 + - + +
604A TYR* 2.8 32.9 + - - -
612A LEU* 4.7 5.6 - - + +
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Residues in contact with GLN 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 PHE* 3.0 48.8 + - + +
104A THR* 3.3 16.9 + - - +
106A TYR* 1.3 79.3 - - + +
108A ASN* 1.3 58.0 + - - +
110A VAL* 3.3 4.9 + - - +
111A ARG* 3.1 49.7 + - - +
294A ARG* 6.1 1.0 - - - +
587A THR 4.3 1.0 - - - +
588A ASP* 3.3 32.5 + - - +
589A LEU* 5.3 2.0 - - - +
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Residues in contact with ASN 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 THR* 3.0 23.9 + - - +
105A GLY 3.7 5.8 - - - +
106A TYR 3.3 0.2 - - - -
107A GLN* 1.3 74.7 - - - +
109A LEU* 1.3 59.9 + - - +
111A ARG* 3.5 19.9 + - - +
112A LEU* 3.1 34.5 + - - +
134A GLU 4.9 0.6 + - - -
135A HIS* 3.2 45.9 + - + +
137A GLN* 2.7 34.9 + - - +
139A LEU* 4.5 3.4 - - + -
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Residues in contact with LEU 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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50A LEU* 4.4 11.3 - - + +
69A ILE* 3.3 36.8 - - + +
70A GLY 4.5 6.5 - - - -
71A TYR* 3.9 28.4 - - + -
98A LEU* 4.0 13.0 - - + +
99A LEU 4.4 0.9 - - - -
100A ALA* 3.6 23.8 - - + +
105A GLY 2.9 16.2 + - - +
106A TYR* 3.3 6.0 + - - +
108A ASN* 1.3 73.6 - - - +
110A VAL* 1.3 66.1 + - - +
112A LEU* 3.4 3.7 + - + +
113A ALA* 3.0 26.0 + - - +
139A LEU* 3.5 24.2 - - + -
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Residues in contact with VAL 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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50A LEU* 4.0 15.9 - - + -
106A TYR* 3.0 50.6 + - + +
107A GLN* 3.5 9.4 - - - +
109A LEU* 1.3 77.1 - - - +
111A ARG* 1.3 52.2 + - - +
113A ALA* 3.6 2.4 + - - +
114A SER* 2.7 36.6 + - - +
587A THR 3.3 18.8 - - - +
588A ASP 4.7 0.2 - - - +
589A LEU 4.0 3.1 - - - +
590A VAL 3.4 11.9 - - - +
591A PRO* 3.3 29.5 - - + +
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Residues in contact with ARG 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 GLN* 3.1 37.6 + - - +
108A ASN* 3.5 24.2 + - - +
109A LEU 3.3 0.2 - - - -
110A VAL* 1.3 73.8 - - - +
112A LEU* 1.3 59.4 + - - +
114A SER* 3.1 0.9 + - - -
115A ARG* 2.9 38.2 + - - +
135A HIS* 3.3 37.1 + - + +
587A THR* 3.6 27.4 - - + +
588A ASP* 2.7 36.1 + - - +
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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
----------------------------------------------------------
71A TYR* 4.3 10.5 - - + -
98A LEU* 4.0 8.7 - - + -
108A ASN 3.1 20.0 + - - +
109A LEU* 3.9 6.1 - - + +
111A ARG* 1.3 75.8 - - - +
113A ALA* 1.3 61.4 + - - +
115A ARG* 3.7 3.3 + - - +
116A ALA* 3.1 16.5 + - - +
127A ILE* 3.3 24.9 - - + +
131A ILE* 3.8 44.2 - - + +
132A LEU* 3.7 20.0 - - + -
135A HIS* 4.0 15.7 - - + +
139A LEU* 3.6 30.1 - - + -
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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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48A GLY 6.3 0.2 - - - -
49A ASN* 5.3 0.7 - - - -
50A LEU* 4.5 9.2 - - + -
71A TYR* 3.6 26.8 + - + -
109A LEU 3.0 18.1 + - - +
110A VAL* 3.6 5.6 - - - +
112A LEU* 1.3 75.6 - - - +
114A SER* 1.3 64.3 + - - +
116A ALA* 3.1 17.5 + - - +
117A TYR* 3.4 12.8 + - - -
591A PRO* 4.1 16.4 - - + -
603A GLN* 4.4 9.4 - - - +
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Residues in contact with SER 114 (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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110A VAL 2.7 20.8 + - - -
111A ARG 3.1 4.5 + - - -
113A ALA* 1.3 78.1 - - - +
115A ARG* 1.3 59.5 + - - +
117A TYR* 3.2 3.6 + - - +
118A LEU* 2.9 45.4 + - - +
587A THR* 3.7 22.7 - - - +
590A VAL 4.3 0.5 + - - -
591A PRO* 3.3 4.7 - - - +
592A LEU* 3.1 33.6 + - - +
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Residues in contact with ARG 115 (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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80A ARG* 3.4 23.8 - - - +
111A ARG* 2.9 22.2 + - + +
112A LEU* 4.2 3.4 - - - +
114A SER* 1.3 75.0 - - - +
116A ALA* 1.3 63.0 + - - +
117A TYR 3.3 0.2 - - - -
118A LEU* 4.6 2.7 - - + -
119A GLU* 3.1 41.7 + - - +
120A GLY* 3.0 20.4 + - - -
126A ARG 4.4 1.0 - - - +
127A ILE* 5.1 0.7 - - - -
131A ILE* 3.3 37.1 - - + +
134A GLU* 2.8 28.7 + - - -
135A HIS* 3.2 27.9 + - - -
587A THR* 5.8 2.2 - - + -
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Residues in contact with ALA 116 (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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48A GLY 5.6 0.2 - - - +
71A TYR* 3.6 14.4 - - - +
112A LEU 3.1 14.2 + - - +
113A ALA 3.1 12.5 + - - +
114A SER 3.1 0.6 - - - -
115A ARG* 1.3 77.6 - - - +
117A TYR* 1.3 57.5 + - + +
120A GLY 3.0 31.0 - - - +
121A PHE 3.2 1.2 + - - -
125A PRO* 3.5 28.4 - - + +
126A ARG 3.5 10.8 - - - -
127A ILE* 3.7 10.1 - - + -
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Residues in contact with TYR 117 (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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18A LEU* 5.8 0.9 - - - +
48A GLY 3.4 27.1 + - - -
49A ASN* 4.0 3.2 + - + +
51A PHE* 3.6 18.7 - + - -
113A ALA* 3.4 11.1 + - + -
114A SER 3.2 5.6 + - - +
116A ALA* 1.3 79.7 - - + +
118A LEU* 1.3 67.7 + - + +
121A PHE* 3.3 47.0 - + - +
125A PRO* 3.8 16.4 - - + +
592A LEU 3.6 13.0 - - - +
593A MET* 4.0 32.4 - - + +
594A ARG* 5.0 6.6 - - + +
603A GLN* 3.2 31.9 - - - -
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Residues in contact with LEU 118 (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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114A SER* 2.9 29.7 + - - +
115A ARG* 4.6 1.3 - - - -
117A TYR* 1.3 79.6 - - + +
119A GLU* 1.3 68.5 + - + +
121A PHE* 5.4 0.2 - - - +
587A THR* 5.5 4.3 - - + +
592A LEU* 4.5 26.7 - - + -
593A MET 4.1 23.6 - - - +
594A ARG* 4.3 30.0 + - + +
600A PRO* 5.8 1.3 - - + -
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Residues in contact with GLU 119 (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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80A ARG* 2.9 42.5 + - - +
81A PHE* 4.7 14.9 - - + -
83A ARG* 5.8 1.6 + - - -
115A ARG* 3.1 44.9 + - - +
118A LEU* 1.3 82.8 - - + +
120A GLY* 1.3 61.0 + - - +
121A PHE 3.3 8.0 + - - +
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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