Contacts of the helix formed by residues 83 - 103 (chain A) in PDB entry 3C2B
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 SER 83 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A VAL* 1.3 76.0 - - - +
84A ALA* 1.3 59.2 + - - +
85A PRO* 3.6 12.5 - - - +
86A GLN* 2.9 35.6 + - - +
87A LEU* 2.9 27.4 + - - +
153A TYR* 3.5 9.0 - - - -
211A GLU* 4.1 5.2 - - - -
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A SER* 1.3 71.2 - - - +
85A PRO* 1.4 67.0 - - + +
87A LEU* 3.2 5.1 + - - +
88A ALA* 2.9 29.1 + - - +
153A TYR* 3.4 25.3 + - + -
208A VAL* 3.9 13.8 - - + +
211A GLU* 3.2 31.5 + - + +
212A LEU* 3.6 16.6 - - + +
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Residues in contact with PRO 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A SER* 3.6 11.7 - - - +
84A ALA* 1.4 92.1 - - + +
86A GLN* 1.3 58.6 + - - +
88A ALA* 3.4 2.2 + - + +
89A ASP* 2.9 40.9 + - - +
211A GLU* 3.7 14.8 - - + +
212A LEU* 3.6 15.8 - - + -
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Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG 4.5 3.7 + - - +
82A VAL* 3.9 21.4 - - + +
83A SER* 2.9 40.6 + - - +
85A PRO* 1.3 75.1 - - - +
87A LEU* 1.3 61.8 + - - +
89A ASP* 3.8 5.9 - - - +
90A HIS* 2.8 49.5 + - + +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 4.0 13.8 - - + +
83A SER 2.9 14.9 + - - +
84A ALA* 3.2 10.1 + - - +
86A GLN* 1.3 77.2 - - - +
88A ALA* 1.3 62.7 - - - +
90A HIS* 3.6 3.2 - - - +
91A LEU* 2.9 54.2 + - + +
144A LEU* 4.0 26.7 - - + +
148A GLY* 4.0 19.3 - - - +
153A TYR* 3.9 27.6 - - + -
154A LEU* 4.2 16.2 - - + -
200A LEU* 4.6 3.4 - - + -
208A VAL* 4.4 9.2 - - + -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA 2.9 15.2 + - - +
85A PRO* 3.8 4.7 - - + +
87A LEU* 1.3 75.3 - - - +
89A ASP* 1.3 67.4 + - - +
91A LEU* 3.3 6.8 + - - +
92A GLU* 3.0 33.2 + - - +
196A VAL* 4.0 11.2 - - + +
200A LEU* 4.5 10.1 - - + -
212A LEU* 4.2 24.2 - - + -
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Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PRO* 2.9 27.8 + - - +
86A GLN* 3.8 6.3 - - - +
88A ALA* 1.3 79.7 - - - +
90A HIS* 1.3 64.2 + - + +
92A GLU* 3.3 12.9 + - - +
93A VAL* 3.0 30.7 + - + +
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Residues in contact with HIS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 5.7 4.3 - - - -
82A VAL* 4.2 17.8 - - + +
86A GLN* 2.8 47.2 + - + +
87A LEU* 3.6 4.5 - - - +
89A ASP* 1.3 76.8 - - + +
91A LEU* 1.3 58.5 + - - +
93A VAL* 3.8 7.5 - - - +
94A PHE* 2.9 30.1 + - - +
140A ARG* 4.4 20.0 + - - +
144A LEU* 3.5 30.8 - - + +
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 2.9 40.1 + - + +
88A ALA* 3.7 4.7 - - - +
89A ASP 3.2 0.2 - - - -
90A HIS* 1.3 74.5 - - - +
92A GLU* 1.3 64.0 + - - +
94A PHE* 3.5 4.3 + - - +
95A ALA* 3.0 19.6 + - - +
141A ALA* 6.4 0.4 - - - -
144A LEU* 3.9 26.9 - - + -
145A ILE* 4.9 6.5 - - + -
154A LEU* 5.5 0.4 - - + -
166A PHE* 3.7 25.8 - - + -
196A VAL* 3.5 24.0 - - + +
199A PHE* 4.0 30.3 - - + -
200A LEU* 4.2 16.4 - - + -
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA* 3.0 24.5 + - - +
89A ASP* 3.3 13.7 + - - +
91A LEU* 1.3 76.9 - - - +
93A VAL* 1.3 63.3 + - + +
95A ALA 3.2 0.9 + - - -
96A HIS* 3.1 21.5 + - - +
189A SER 5.1 1.0 - - - +
192A ALA* 3.5 14.8 - - + +
193A LYS* 2.7 52.3 + - - +
196A VAL* 3.6 24.8 - - + +
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ASP* 3.0 20.3 + - + +
90A HIS* 4.0 8.1 - - - +
92A GLU* 1.3 73.0 - - + +
94A PHE* 1.3 67.7 + - - +
96A HIS* 3.4 5.8 + - - +
97A ASP* 2.9 45.7 + - - +
140A ARG* 5.5 6.5 - - - +
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Residues in contact with PHE 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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75A PHE* 5.8 1.1 - + - -
90A HIS 2.9 20.0 + - - +
91A LEU 3.5 4.0 - - - +
93A VAL* 1.3 77.1 - - - +
95A ALA* 1.3 62.3 + - - +
97A ASP* 3.1 9.9 + - + +
98A LEU* 2.8 37.8 + - + +
137A ILE* 3.4 46.4 - - + -
140A ARG* 3.8 25.9 - - + +
141A ALA* 3.4 27.6 - - + -
144A LEU* 3.9 13.5 - - + -
163A TYR* 4.0 13.2 - + - -
166A PHE* 3.6 22.2 - + - -
170A ILE* 4.0 17.3 - - + -
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Residues in contact with ALA 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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91A LEU 3.0 17.5 + - - +
92A GLU 3.2 0.4 + - - -
94A PHE* 1.3 82.6 - - - +
96A HIS* 1.3 58.3 + - - +
98A LEU* 3.3 3.7 + - - +
99A LEU* 3.1 32.0 + - - +
166A PHE* 4.4 2.9 - - + -
170A ILE* 3.6 33.1 - - + +
192A ALA* 3.5 29.8 - - + +
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Residues in contact with HIS 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 GLU 3.1 16.4 + - - +
93A VAL* 3.8 5.8 - - + +
95A ALA* 1.3 73.9 - - - +
97A ASP* 1.3 62.2 + - - +
99A LEU* 3.3 6.8 + - - +
100A ASP* 3.0 35.0 + - + +
188A PHE* 3.5 29.0 - + + +
189A SER* 3.8 33.1 + - - -
192A ALA* 3.7 9.6 - - + +
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Residues in contact with ASP 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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73A ARG* 4.5 9.5 + - - -
75A PHE* 3.7 32.9 - - + -
93A VAL* 2.9 39.2 + - - +
94A PHE* 3.4 7.5 - - - +
96A HIS* 1.3 78.1 - - - +
98A LEU* 1.3 56.9 + - - +
100A ASP* 3.4 6.5 + - - +
101A VAL* 2.8 35.0 + - + +
137A ILE* 4.7 2.5 - - + -
140A ARG* 5.4 2.8 + - - -
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Residues in contact with LEU 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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94A PHE* 2.8 33.0 + - + +
95A ALA 3.5 9.0 - - - +
97A ASP* 1.3 72.5 - - - +
99A LEU* 1.3 57.6 + - - +
101A VAL* 3.2 5.3 + - + +
102A LEU* 2.8 59.0 + - + +
134A ARG* 4.8 2.0 - - + -
137A ILE* 4.0 28.8 - - + +
167A TYR* 3.7 36.6 - - + +
170A ILE* 4.1 20.6 - - + -
171A VAL* 3.8 15.7 - - + -
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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
----------------------------------------------------------
95A ALA 3.1 19.0 + - - +
96A HIS* 3.6 6.1 - - - +
98A LEU* 1.3 74.1 - - - +
100A ASP* 1.3 57.4 + - - +
102A LEU* 3.2 7.6 + - + +
103A ALA* 2.9 31.2 + - - +
170A ILE* 3.6 30.3 - - + +
171A VAL* 4.3 12.6 - - + -
174A LEU* 3.8 27.1 - - + -
178A MSE 4.6 1.4 - - + +
188A PHE* 3.8 42.4 - - + +
191A ARG* 3.7 26.5 - - + -
192A ALA 4.5 1.8 - - - +
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Residues in contact with ASP 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 HIS* 3.0 25.8 + - + +
97A ASP* 3.5 7.6 - - - +
99A LEU* 1.3 74.9 - - - +
101A VAL* 1.3 65.5 + - + +
103A ALA* 3.5 3.1 + - - +
104A GLY* 3.3 18.5 + - - -
186A LYS* 5.8 1.6 + - - -
188A PHE* 4.0 18.8 - - + -
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Residues in contact with VAL 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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73A ARG* 6.1 2.9 - - + -
75A PHE* 4.6 12.8 - - + -
97A ASP* 2.8 24.9 + - - +
98A LEU* 3.6 7.6 - - + +
100A ASP* 1.3 73.5 - - + +
102A LEU* 1.3 74.6 + - + +
104A GLY* 3.2 10.6 + - - -
107A SER* 3.7 20.0 + - - +
133A GLY 6.2 0.4 - - - +
134A ARG* 5.9 4.5 - - + -
137A ILE* 4.4 23.1 - - + -
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Residues in contact with LEU 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 LEU* 2.8 40.9 + - + +
99A LEU* 3.7 7.0 - - + +
101A VAL* 1.3 81.4 - - + +
103A ALA* 1.3 58.9 - - - +
104A GLY 3.2 2.0 + - - +
107A SER* 4.2 7.7 + - - +
108A LEU* 3.3 26.3 - - - +
134A ARG* 5.1 7.4 - - + -
167A TYR* 3.9 14.6 - - - +
171A VAL* 3.5 41.7 - - + -
175A HIS* 3.7 35.6 + - + +
178A MSE 3.7 13.5 - - + -
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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
----------------------------------------------------------
99A LEU 2.9 17.4 + - - +
100A ASP* 3.9 4.9 - - - +
101A VAL 3.3 0.2 - - - -
102A LEU* 1.3 74.0 - - - +
104A GLY* 1.3 63.3 + - - +
105A ASP* 3.6 1.6 + - - +
108A LEU* 3.6 10.8 - - - +
178A MSE 3.6 27.6 - - - -
184A PRO* 4.5 7.0 - - + -
188A PHE* 3.9 18.6 - - + -
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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
------------------------------------------------------------
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