Contacts of the helix formed by residues 76 - 88 (chain A) in PDB entry 1CG4
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 PRO 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A LEU* 3.3 12.5 - - + +
75A SER* 1.4 82.8 - - - +
77A ALA* 1.3 64.3 + - - +
79A LEU* 3.2 1.1 + - + +
80A MET* 2.9 30.9 + - - +
105A LEU* 4.1 20.6 - - + -
106A ILE 3.4 15.0 - - - +
107A LEU* 4.2 15.0 - - + -
151A LEU* 6.2 1.1 - - + -
189A ASP 6.4 0.2 - - - -
190A THR* 5.3 9.9 - - + +
193A VAL* 3.8 25.6 - - + -
197A LEU* 4.2 18.4 - - + -
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Residues in contact with ALA 77 (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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75A SER* 3.2 7.8 - - - +
76A PRO* 1.3 81.3 - - - +
78A ALA* 1.3 57.3 + - - +
80A MET* 3.4 5.9 + - - +
81A LYS* 2.9 30.2 + - - +
108A ASP* 6.2 0.2 - - - +
193A VAL* 6.1 0.9 - - - -
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Residues in contact with ALA 78 (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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37A HIS* 3.7 32.5 - - + +
54A LEU* 4.5 4.5 - - + -
75A SER* 2.9 27.0 + - - +
77A ALA* 1.3 75.6 - - - +
79A LEU* 1.3 68.1 + - - +
81A LYS* 3.3 7.2 + - - +
82A GLU* 3.0 31.4 + - - +
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Residues in contact with LEU 79 (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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54A LEU* 3.9 12.3 - - + +
55A ILE* 3.8 18.8 - - + -
68A ILE* 4.4 3.1 - - + -
74A LEU* 3.8 17.7 - - + -
75A SER 2.7 14.7 + - - +
76A PRO 3.6 7.4 - - - +
78A ALA* 1.3 73.5 - - - +
80A MET* 1.3 56.1 + - + +
82A GLU* 3.1 4.6 + - - -
83A MET* 2.8 48.9 + - + +
97A LEU* 3.8 23.3 - - + -
99A LEU* 3.8 25.8 - - + -
197A LEU* 4.0 16.6 - - + -
200A MET* 3.9 15.0 - - + -
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Residues in contact with MET 80 (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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76A PRO 2.9 21.8 + - - +
77A ALA* 3.6 6.1 - - - +
79A LEU* 1.3 81.8 - - + +
81A LYS* 1.3 63.7 + - - +
83A MET* 3.4 11.1 + - - +
84A LYS* 3.0 26.7 + - - +
193A VAL* 3.4 30.3 - - + -
196A ILE* 3.9 41.1 - - + -
197A LEU* 3.2 35.2 - - + -
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Residues in contact with LYS 81 (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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53A HIS* 6.3 1.2 - - - -
77A ALA 2.9 18.3 + - - +
78A ALA* 3.6 8.1 - - - +
79A LEU 3.2 0.2 - - - -
80A MET* 1.3 76.7 - - - +
82A GLU* 1.3 64.0 + - + +
84A LYS* 3.8 4.8 - - - +
85A GLU* 2.6 58.7 + - + +
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Residues in contact with GLU 82 (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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37A HIS* 4.4 3.5 - - - +
51A VAL 5.1 3.8 - - - +
52A LEU* 3.7 7.8 - - + +
53A HIS* 2.8 45.6 + - + +
54A LEU* 3.1 31.4 + - - +
55A ILE* 3.4 26.3 + - + +
78A ALA* 3.0 20.4 + - - +
79A LEU* 3.7 2.9 - - - +
81A LYS* 1.3 76.7 - - + +
83A MET* 1.3 67.8 + - - +
85A GLU* 3.0 16.1 + - - +
86A LEU* 2.9 28.3 + - + +
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Residues in contact with MET 83 (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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55A ILE* 3.9 2.0 - - + +
79A LEU* 2.8 42.2 + - + +
80A MET* 3.7 12.8 - - - +
82A GLU* 1.3 72.2 - - - +
84A LYS* 1.3 65.8 + - - +
86A LEU* 3.0 1.7 + - - +
87A GLU* 2.8 31.0 + - - +
93A VAL* 3.8 28.3 - - + -
94A ARG* 3.0 50.0 - - + +
196A ILE* 4.2 8.5 - - + -
200A MET* 3.7 32.8 - - - +
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Residues in contact with LYS 84 (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 MET 3.0 17.7 + - - +
81A LYS* 3.8 5.8 - - - +
83A MET* 1.3 76.6 - - - +
85A GLU* 1.3 66.8 + - + +
87A GLU* 3.2 15.2 + - - +
88A ASP* 2.8 61.0 + - - +
94A ARG* 5.6 0.2 - - - +
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Residues in contact with GLU 85 (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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51A VAL 5.3 4.3 - - - +
81A LYS* 2.6 49.0 + - + +
82A GLU* 3.0 17.7 + - - +
84A LYS* 1.3 81.6 - - + +
86A LEU* 1.3 64.7 + - + +
88A ASP* 3.7 8.1 + - - +
89A ARG* 3.1 32.1 + - - +
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Residues in contact with LEU 86 (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 THR* 4.0 27.6 - - + -
51A VAL 5.7 1.6 - - - +
52A LEU* 4.0 12.8 - - + -
55A ILE* 3.7 21.1 - - + -
59A ILE* 3.9 21.5 - - + -
60A LEU* 4.9 2.0 - - + -
82A GLU* 2.9 15.2 + - + +
83A MET 3.7 0.4 - - - +
85A GLU* 1.3 77.5 - - + +
87A GLU* 1.3 60.7 + - - +
89A ARG* 3.0 24.7 + - - +
90A GLY 3.4 0.3 + - - -
91A ILE* 2.9 38.2 + - + +
93A VAL* 3.6 29.4 - - + -
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Residues in contact with GLU 87 (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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83A MET* 2.8 25.6 + - - +
84A LYS* 3.5 15.7 + - - +
86A LEU* 1.3 72.0 - - - +
88A ASP* 1.3 67.9 + - - +
89A ARG 2.9 1.6 - - - -
90A GLY* 3.0 14.2 + - - -
91A ILE 3.2 19.4 + - - +
92A PRO* 4.7 3.2 - - + +
93A VAL* 4.2 5.9 + - + +
94A ARG* 2.6 56.7 + - - +
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Residues in contact with ASP 88 (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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84A LYS* 2.8 56.2 + - - +
85A GLU* 4.0 7.7 - - - +
86A LEU 3.3 0.2 - - - -
87A GLU* 1.3 78.0 - - - +
89A ARG* 1.3 60.4 + - + +
90A GLY 3.3 2.7 + - - -
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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