Contacts of the helix formed by residues 95 - 109 (chain A) in PDB entry 4IVR
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 GLU 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A TRP 3.8 3.8 + - - -
89A ARG* 2.7 72.3 + - - +
90A VAL* 5.8 0.2 - - - +
93A ALA 3.5 1.2 + - - -
94A SER* 1.3 82.8 - - - +
96A THR* 1.3 60.0 + - - +
97A ILE 3.2 2.9 - - - -
98A ALA* 3.1 18.8 + - + +
99A ASN* 2.9 24.6 + - - +
223A PRO 3.7 10.9 - - - +
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Residues in contact with THR 96 (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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88A TRP* 2.7 23.9 + - - -
93A ALA* 4.2 14.1 + - + +
94A SER 3.5 2.2 - - - -
95A GLU* 1.3 73.1 - - - +
97A ILE* 1.3 62.6 + - - +
99A ASN* 3.2 8.0 + - + +
100A ILE* 3.0 25.3 + - + +
124A ALA* 3.6 39.5 - - + +
127A THR* 4.0 18.7 - - + +
128A MET* 3.7 21.1 - - + -
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Residues in contact with ILE 97 (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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85A MET* 4.6 8.3 - - - -
88A TRP* 4.0 19.3 - - + -
89A ARG* 5.6 2.7 - - + -
95A GLU 5.5 0.2 - - - -
96A THR* 1.3 75.6 - - - +
98A ALA* 1.3 62.5 + - - +
100A ILE* 3.2 13.0 + - - +
101A TYR* 3.1 45.6 + - + -
128A MET* 3.6 32.8 - - + -
223A PRO* 3.3 34.8 - - + +
225A GLU* 4.1 8.7 - - + +
501A N50 4.0 22.9 - - - -
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Residues in contact with ALA 98 (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 GLU* 3.1 25.2 + - + +
97A ILE* 1.3 80.4 - - - +
99A ASN* 1.3 61.9 + - - +
100A ILE 3.3 0.2 + - - -
101A TYR* 3.5 1.4 + - - +
102A THR* 2.9 30.1 + - - +
223A PRO 3.3 10.3 + - - +
224A GLY* 3.7 20.2 - - - +
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Residues in contact with ASN 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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94A SER 4.7 4.7 - - - +
95A GLU 2.9 13.0 + - - +
96A THR* 3.2 11.5 + - - +
98A ALA* 1.3 75.8 - - - +
100A ILE* 1.3 60.5 + - - +
102A THR* 3.6 5.3 + - - -
103A THR* 2.8 39.0 + - - -
120A VAL* 4.0 20.2 + - - +
124A ALA* 4.5 13.3 - - - +
119B VAL* 5.8 5.5 - - - +
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Residues in contact with ILE 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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96A THR* 3.0 17.5 + - + +
97A ILE* 3.2 8.5 + - - +
99A ASN* 1.3 77.2 - - - +
101A TYR* 1.3 65.8 + - + +
103A THR* 3.4 1.9 + - - -
104A GLN* 3.2 18.9 + - - +
120A VAL* 5.7 2.0 - - + -
121A MET* 3.3 24.8 - - - +
124A ALA* 3.7 29.8 - - + -
125A GLN* 4.5 11.0 - - + -
128A MET* 4.1 20.6 - - + -
176A ARG* 3.3 35.9 - - - +
501A N50 3.8 20.0 - - - +
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Residues in contact with TYR 101 (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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58A HIS* 3.9 13.4 + - - -
97A ILE* 3.1 39.3 + - + +
98A ALA 4.3 0.2 - - - +
100A ILE* 1.3 75.9 - - + +
102A THR* 1.3 63.6 + - - +
104A GLN* 4.0 4.7 - - + +
105A HIS* 3.2 25.1 + - - +
176A ARG* 3.5 18.4 + - - -
224A GLY 4.2 4.9 - - - +
225A GLU* 3.4 46.7 + - + -
226A ARG* 3.9 41.7 + - + +
228A ASP* 4.7 13.5 - - + -
231A MET* 4.7 10.2 - - + +
501A N50 3.3 33.0 + - - -
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Residues in contact with THR 102 (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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98A ALA* 2.9 23.4 + - - +
99A ASN* 3.8 7.0 - - - -
100A ILE 3.3 0.2 - - - -
101A TYR* 1.3 76.2 - - - +
103A THR* 1.3 59.8 + - - +
105A HIS* 3.5 3.9 + - - +
106A ARG* 3.0 28.3 + - + +
226A ARG* 4.1 25.0 + - - +
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Residues in contact with THR 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 ASN* 2.8 31.3 + - - -
100A ILE 3.8 3.8 - - - -
101A TYR 3.3 0.2 - - - -
102A THR* 1.3 79.0 - - - +
104A GLN* 1.3 60.1 + - - +
106A ARG* 3.4 4.6 + - - -
107A LEU* 2.9 24.6 + - - +
112A ILE* 3.5 24.0 - - + +
117A ALA* 4.0 13.9 - - + +
120A VAL* 3.5 32.8 - - + +
121A MET* 4.4 6.3 - - + -
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Residues in contact with GLN 104 (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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100A ILE 3.2 9.7 + - - +
101A TYR* 4.0 6.3 - - + +
102A THR 3.4 0.2 - - - -
103A THR* 1.3 73.6 - - - +
105A HIS* 1.3 61.7 - - - +
107A LEU* 3.2 16.2 + - - +
108A ASP* 2.9 53.3 + - - +
121A MET* 3.6 8.1 - - + +
176A ARG* 2.9 32.3 + - - +
179A MET* 3.4 36.6 + - + +
181A SER* 2.8 26.2 + - - -
228A ASP* 3.7 19.5 - - - +
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Residues in contact with HIS 105 (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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101A TYR 3.2 17.7 + - - +
102A THR 3.6 4.6 + - - +
104A GLN* 1.3 79.9 - - - +
106A ARG* 1.3 58.3 + - - +
108A ASP* 3.3 9.8 + - + +
109A GLN* 2.9 69.5 + - + +
226A ARG* 3.1 42.2 + - - +
228A ASP* 5.9 0.9 - - - -
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Residues in contact with ARG 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 THR* 3.0 20.4 + - + +
103A THR* 3.7 7.2 - - - +
104A GLN 3.3 0.2 - - - -
105A HIS* 1.3 78.3 + - - +
107A LEU* 1.3 59.5 + - - +
109A GLN* 3.3 4.9 + - - -
110A GLY 3.2 4.5 + - - -
111A GLU* 2.8 44.1 + - + +
112A ILE* 4.0 16.8 - - + -
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Residues in contact with LEU 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 THR 2.9 15.0 + - - +
104A GLN* 3.2 28.0 + - - +
106A ARG* 1.3 75.4 - - - +
108A ASP* 1.3 64.9 + - - +
110A GLY* 3.2 12.5 + - - -
112A ILE* 3.7 16.7 - - + +
113A SER* 3.7 31.2 - - - +
114A ALA* 3.8 9.0 - - + +
117A ALA* 4.1 6.3 - - + -
179A MET 4.1 2.9 - - - +
180A GLY 3.5 24.7 - - - +
181A SER* 3.8 13.0 - - - -
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Residues in contact with ASP 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 GLN* 2.9 43.0 + - - +
105A HIS* 3.6 11.9 - - + +
107A LEU* 1.3 74.9 - - - +
109A GLN* 1.3 61.3 + - + +
110A GLY* 2.9 10.5 + - - -
179A MET* 4.5 11.6 - - - +
228A ASP* 4.5 6.8 - - - +
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Residues in contact with GLN 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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105A HIS* 2.9 60.6 + - + +
106A ARG* 3.3 8.5 + - - +
108A ASP* 1.3 74.6 - - + +
110A GLY* 1.3 60.1 + - - +
111A GLU* 3.7 6.8 + - + +
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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
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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