Contacts of the helix formed by residues 91 - 109 (chain A) in PDB entry 1C1D
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 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A SER 3.4 6.6 + - - +
90A ILE* 1.3 76.8 - - - +
92A PRO* 1.3 73.7 - - + +
93A SER* 3.2 10.0 + - - -
94A THR* 2.7 45.0 + - - -
95A TRP* 3.0 17.8 + - - +
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Residues in contact with PRO 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE 4.4 0.9 - - - +
91A ASP* 1.3 87.9 - - + +
93A SER* 1.3 57.7 + - - +
95A TRP* 3.9 7.2 - - + +
96A ALA* 2.9 31.0 + - - +
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASP* 3.1 10.3 + - - -
92A PRO* 1.3 76.3 - - - +
94A THR* 1.3 65.9 + - - +
96A ALA* 3.3 6.3 + - - +
97A ARG* 3.0 23.8 + - - +
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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
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21A THR* 3.8 33.5 - - + +
84A PRO* 5.2 1.8 - - + -
90A ILE* 3.8 20.6 - - + -
91A ASP* 2.7 29.4 + - - -
93A SER* 1.3 74.5 - - - +
95A TRP* 1.3 56.6 + - - +
97A ARG* 3.2 3.5 + - - +
98A ILE* 2.9 36.6 + - + +
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Residues in contact with TRP 95 (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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43A ALA* 3.9 20.9 - - + -
81A ILE* 5.0 2.2 - - + -
83A LEU* 4.1 19.1 - - + -
87A ARG* 3.4 53.3 - - - +
90A ILE* 3.6 12.0 - - + +
91A ASP 3.0 15.4 + - - +
92A PRO* 3.9 7.4 - - + +
94A THR* 1.3 75.0 - - - +
96A ALA* 1.4 65.1 + - - +
98A ILE* 3.2 23.1 + - + +
99A LEU* 3.0 47.6 + - + +
120A ASN 3.8 6.7 - - - -
121A THR* 4.1 7.2 - - + -
125A ASP* 2.9 42.0 + - - -
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Residues in contact with ALA 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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92A PRO 2.9 21.1 + - - +
93A SER* 3.7 6.7 - - - +
95A TRP* 1.4 78.7 - - - +
97A ARG* 1.3 58.2 + - - +
99A LEU* 3.4 7.6 + - - +
100A ARG* 3.0 27.7 + - - +
128A THR* 5.0 9.4 - - + +
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Residues in contact with ARG 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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18A ASP* 2.9 36.3 + - - -
20A MET* 3.4 43.1 - - - +
21A THR* 3.5 17.0 - - + -
93A SER 3.0 17.0 + - - +
94A THR* 3.2 4.9 + - - +
96A ALA* 1.3 73.3 - - - +
98A ILE* 1.3 67.6 + - - +
100A ARG* 3.1 34.0 + - - +
101A ILE* 3.0 36.4 + - + +
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Residues in contact with ILE 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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21A THR* 4.0 11.9 - - + +
23A ALA* 4.0 25.4 - - + -
25A PHE* 3.3 18.6 - - + -
81A ILE* 3.8 33.7 - - + -
83A LEU* 4.2 17.5 - - + -
84A PRO* 4.6 5.2 - - + -
90A ILE* 4.6 3.4 - - + -
94A THR* 2.9 36.0 + - + +
95A TRP* 3.2 21.5 + - + +
97A ARG* 1.3 78.1 - - - +
99A LEU* 1.3 58.2 + - - +
101A ILE* 3.4 0.8 + - - -
102A HIS* 3.0 24.8 + - - +
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Residues in contact with LEU 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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41A THR* 5.8 0.4 - - + -
81A ILE* 4.8 11.7 - - + -
95A TRP* 3.0 64.7 + - + +
96A ALA* 3.9 4.7 - - - +
98A ILE* 1.3 73.6 - - - +
100A ARG* 1.3 62.7 + - - +
102A HIS* 4.3 2.2 - - + -
103A ALA* 2.8 26.7 + - - +
121A THR* 5.2 4.3 - - + -
125A ASP* 3.6 25.4 - - + +
126A MET* 5.9 0.2 - - + -
128A THR* 3.9 31.4 - - + +
129A LEU* 3.2 29.4 - - + +
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Residues in contact with ARG 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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16A ARG* 4.6 5.3 - - - +
96A ALA 3.0 14.7 + - - +
97A ARG* 3.1 44.3 + - - +
99A LEU* 1.3 75.8 - - - +
101A ILE* 1.3 77.8 + - - +
103A ALA* 3.2 7.6 + - - +
104A GLU* 2.8 64.3 + - + +
128A THR* 5.3 3.3 - - + +
132A THR* 4.4 15.1 - - + +
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Residues in contact with ILE 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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16A ARG* 3.6 37.5 - - - +
18A ASP* 3.5 37.5 - - + +
25A PHE* 3.5 23.8 - - + -
97A ARG* 3.0 35.1 + - + +
98A ILE* 3.6 4.5 - - - +
100A ARG* 1.3 92.9 - - - +
102A HIS* 1.3 64.6 + - - +
104A GLU* 3.0 9.8 + - - +
105A ASN* 3.0 22.3 + - - +
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Residues in contact with HIS 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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25A PHE* 3.9 15.6 - - + +
26A VAL 5.4 0.2 - - - -
27A ILE* 4.2 10.7 - - + +
41A THR* 2.8 38.4 + - + +
79A SER* 3.1 30.1 - - - -
81A ILE* 4.1 11.8 - - + +
98A ILE 3.0 17.0 + - - +
99A LEU* 3.6 7.2 - - + +
101A ILE* 1.3 74.8 - - - +
103A ALA* 1.4 63.2 + - - +
105A ASN* 3.0 11.7 + - - +
106A ILE* 2.9 47.8 + - + +
129A LEU* 3.8 22.4 - - + -
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Residues in contact with ALA 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 LEU 2.8 17.9 + - - +
100A ARG* 3.6 3.8 - - - +
101A ILE 3.2 0.2 - - - -
102A HIS* 1.4 77.5 - - - +
104A GLU* 1.3 56.6 + - - +
106A ILE* 3.3 4.4 + - - +
107A ASP* 2.9 30.5 + - - +
129A LEU* 3.6 26.0 - - + +
132A THR* 3.4 31.0 - - - +
133A THR* 3.7 10.7 - - + -
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Residues in contact with GLU 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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16A ARG* 2.9 31.3 + - - +
100A ARG* 2.8 53.7 + - + +
101A ILE* 3.0 8.3 + - - +
103A ALA* 1.3 75.9 - - - +
105A ASN* 1.4 64.1 + - - +
107A ASP* 3.3 8.5 + - - +
108A LYS* 3.1 38.5 + - - +
132A THR* 4.2 11.0 - - + +
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Residues in contact with ASN 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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14A VAL* 4.7 14.2 - - + +
16A ARG* 3.0 49.3 + - - +
25A PHE* 3.8 27.9 - - - +
27A ILE* 4.0 16.9 - - + +
101A ILE 3.0 11.7 + - - -
102A HIS* 3.0 11.2 + - - +
104A GLU* 1.4 74.7 - - - +
106A ILE* 1.3 65.7 + - - +
107A ASP 3.3 0.2 + - - -
108A LYS* 3.3 18.1 + - - +
109A LEU* 3.6 13.9 + - - +
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Residues in contact with ILE 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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27A ILE* 4.1 11.9 - - + -
102A HIS* 2.9 51.0 + - + +
103A ALA* 3.6 11.2 - - - +
105A ASN* 1.3 76.7 - - - +
107A ASP* 1.4 63.9 + - - +
109A LEU* 3.0 22.2 + - - +
110A SER 3.6 2.8 + - - -
113A TYR* 3.9 28.2 - - + +
115A THR* 3.7 23.8 - - + -
129A LEU* 4.5 3.6 - - + -
133A THR* 3.9 17.7 - - + +
135A PHE* 4.0 18.0 - - + +
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Residues in contact with ASP 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 ALA 2.9 17.9 + - - +
104A GLU* 3.6 9.2 - - - +
105A ASN 3.1 0.2 - - - -
106A ILE* 1.4 79.0 - - - +
108A LYS* 1.3 62.6 + - + +
110A SER* 2.9 19.1 + - - -
132A THR* 4.1 11.3 - - + +
133A THR* 2.8 31.1 + - - +
134A GLU 4.3 0.9 + - - -
135A PHE* 3.7 13.1 - - - -
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Residues in contact with LYS 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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16A ARG* 5.0 4.8 - - - +
104A GLU* 3.1 31.3 + - - +
105A ASN* 3.8 11.1 + - - +
106A ILE 3.3 0.8 - - - -
107A ASP* 1.3 76.7 - - + +
109A LEU* 1.3 61.0 + - + +
110A SER* 2.9 14.6 + - - -
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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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12A MET* 3.9 26.9 - - - -
14A VAL* 4.1 22.4 - - + -
27A ILE* 4.3 24.2 - - + -
29A LEU* 4.4 10.8 - - + -
105A ASN 3.6 9.4 + - - +
106A ILE 3.0 9.6 + - - +
108A LYS* 1.3 78.4 - - + +
110A SER* 1.3 65.6 - - - +
111A GLY 3.3 1.8 - - - -
112A ASN* 2.9 37.4 + - + +
113A TYR* 3.9 31.6 - - + +
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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