Contacts of the helix formed by residues 91 - 108 (chain A) in PDB entry 3C07
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLU* 4.6 1.6 + - - +
90A THR* 1.3 80.2 + - - +
92A LEU* 1.3 57.4 + - - +
93A GLU* 3.0 37.0 + - - +
94A ALA* 2.9 15.9 + - + +
95A ARG* 2.7 35.6 + - - +
154A LYS* 5.2 2.5 - - - +
155A THR* 5.9 2.0 - - - -
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Residues in contact with LEU 92 (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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90A THR 3.6 3.2 + - - -
91A ASP* 1.3 72.6 + - - +
93A GLU* 1.3 67.3 + - - +
95A ARG* 2.9 6.5 + - - +
96A LEU* 2.8 27.9 + - + +
149A VAL* 3.7 27.1 - - + +
150A LEU* 4.7 10.8 - - + -
153A ALA* 3.7 25.9 - - + +
154A LYS 4.9 1.0 - - - +
155A THR* 4.3 22.9 + - + +
157A VAL* 5.8 0.2 - - + -
169A MSE 5.7 2.7 - - - -
203A ALA* 3.9 26.0 - - + +
206A VAL* 3.4 35.0 - - + -
207A VAL* 5.1 0.2 - - + -
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASP* 3.0 14.2 + - - +
92A LEU* 1.3 83.3 - - - +
94A ALA* 1.3 55.3 + - - +
96A LEU* 2.8 3.8 + - - +
97A ALA* 2.6 37.7 + - + +
196A GLU 5.0 1.7 - - - +
199A ALA* 4.2 17.4 - - + +
200A ARG* 2.8 45.2 + - - +
203A ALA* 3.8 17.8 - - + +
204A ARG* 5.0 7.0 + - - -
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 4.6 1.4 - - - +
89A GLU* 3.5 31.6 - - + +
91A ASP* 2.9 21.2 + - + +
93A GLU* 1.3 77.9 - - - +
95A ARG* 1.3 57.6 + - - +
97A ALA* 3.4 9.3 - - - +
98A GLY* 3.0 25.6 + - - -
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Residues in contact with ARG 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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85A VAL* 5.0 3.7 - - - +
86A LEU* 3.2 55.2 + - + +
87A ALA 5.4 0.2 - - - -
89A GLU* 2.9 40.9 + - + +
90A THR 4.2 2.2 - - - -
91A ASP 2.7 20.7 + - - +
92A LEU 3.3 6.5 - - - +
94A ALA* 1.3 70.2 - - - +
96A LEU* 1.3 64.6 + - - +
98A GLY* 4.0 0.3 - - - -
99A VAL* 3.0 31.1 + - - +
148A ALA* 2.9 24.5 + - - +
149A VAL* 3.2 25.4 + - + -
152A GLY* 3.3 28.4 + - - -
153A ALA* 4.1 9.0 - - - +
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Residues in contact with LEU 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 LEU* 2.8 21.7 + - + +
93A GLU* 2.8 8.0 + - - +
95A ARG* 1.3 74.1 - - - +
97A ALA* 1.3 65.2 + - - +
99A VAL* 3.3 4.0 + - + +
100A LEU* 3.0 57.1 + - + +
146A HIS* 4.3 15.9 - - + +
149A VAL* 4.1 19.2 - - + +
169A MSE 5.0 8.5 - - + -
199A ALA* 4.1 14.1 - - + +
202A THR* 3.6 35.7 - - + -
203A ALA* 4.9 2.0 - - + +
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Residues in contact with ALA 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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93A GLU* 2.6 23.8 + - + +
94A ALA* 3.4 12.8 - - - +
96A LEU* 1.3 71.5 - - - +
98A GLY* 1.3 61.5 + - - +
100A LEU* 3.4 2.8 + - - +
101A LYS* 3.1 23.7 + - - +
195A ALA* 4.8 5.1 - - - +
196A GLU* 5.5 12.3 - - + +
199A ALA* 3.7 18.9 - - + +
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Residues in contact with GLY 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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85A VAL* 3.6 27.1 - - - -
94A ALA 3.0 9.8 + - - -
97A ALA* 1.3 72.7 - - - +
99A VAL* 1.3 67.5 + - - +
100A LEU 2.9 0.9 + - - -
101A LYS* 3.0 9.6 + - - +
102A VAL* 2.8 28.7 + - - +
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Residues in contact with VAL 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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78A HIS* 2.7 44.1 + - + +
82A VAL* 4.0 21.5 - - + -
85A VAL* 4.4 4.6 - - + +
86A LEU* 3.9 18.2 - - + -
95A ARG 3.0 21.3 + - - +
96A LEU* 3.5 5.6 - - + +
98A GLY* 1.3 73.7 - - - +
100A LEU* 1.3 65.7 + - + +
102A VAL* 3.5 1.9 + - - +
103A TRP 3.2 5.9 + - - -
145A ILE* 4.2 11.2 - - + -
146A HIS* 4.3 20.9 - - + -
149A VAL* 3.6 21.3 - - + -
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Residues in contact with LEU 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 LEU* 3.0 42.2 + - + +
97A ALA 3.7 3.6 - - - +
99A VAL* 1.3 75.9 - - + +
101A LYS* 1.3 62.2 + - - +
103A TRP* 3.0 21.9 - - - +
104A LEU* 3.1 18.2 + - - +
146A HIS* 4.3 7.9 - - + -
169A MSE 5.5 0.7 - - - +
172A SER* 6.3 3.1 - - - -
173A GLN* 3.9 43.5 - - + +
176A LEU* 4.1 17.5 - - + -
195A ALA* 4.0 25.4 - - + +
198A GLY 5.6 1.1 - - - -
199A ALA* 4.5 4.7 - - + +
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Residues in contact with LYS 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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97A ALA 3.1 12.0 + - - +
98A GLY* 3.3 13.2 - - - +
100A LEU* 1.3 77.4 - - - +
102A VAL* 1.3 68.8 + - + +
103A TRP 3.1 0.2 - - - -
104A LEU* 3.0 13.4 + - - +
105A ASP* 3.0 35.2 + - - +
192A TYR* 4.3 23.8 - - + -
195A ALA* 4.7 4.7 - - + +
196A GLU* 6.1 0.7 - - - +
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Residues in contact with VAL 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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78A HIS* 4.0 10.8 - - + -
81A ALA* 3.3 41.7 - - + +
82A VAL* 4.4 1.6 - - + +
85A VAL* 4.5 15.7 - - + -
98A GLY* 2.8 24.6 + - - +
99A VAL* 3.9 6.5 - - - +
101A LYS* 1.3 73.9 - - + +
103A TRP* 1.3 65.8 + - - +
105A ASP* 3.4 16.7 + - + +
106A ILE* 3.1 23.2 + - + +
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Residues in contact with TRP 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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74A ILE* 4.2 39.5 - - + -
75A ALA* 5.4 2.5 - - - -
78A HIS* 3.3 45.1 - + + +
99A VAL 3.2 5.5 + - - +
100A LEU* 3.0 16.8 - - - +
102A VAL* 1.3 78.6 - - - +
104A LEU* 1.3 76.0 + - + +
106A ILE* 3.2 4.2 + - + +
107A ALA* 2.8 41.2 + - + +
142A ALA* 6.3 2.2 - - + -
173A GLN* 3.4 24.0 - - + +
174A MSE 4.7 6.1 - - + -
176A LEU* 4.5 8.0 - - + +
177A VAL* 3.5 35.6 - - + +
180A TRP* 5.8 1.7 - + - -
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Residues in contact with LEU 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 LEU 3.1 25.4 + - - +
101A LYS* 3.0 9.7 + - - +
103A TRP* 1.3 90.4 - - + +
105A ASP* 1.3 57.9 + - - +
106A ILE 3.0 0.3 + - - -
107A ALA* 3.0 2.5 + - + +
108A THR* 2.7 30.9 + - - +
176A LEU* 3.3 30.3 - - + -
180A TRP* 3.5 44.4 + - + +
191A SER* 4.8 5.8 - - - +
192A TYR* 3.5 32.1 - - + +
195A ALA* 4.1 12.1 - - + -
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Residues in contact with ASP 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 LYS* 3.0 28.1 + - - +
102A VAL* 3.4 19.9 + - + +
104A LEU* 1.3 74.4 - - - +
106A ILE* 1.3 63.8 - - + +
108A THR* 3.4 15.7 - - - -
109A PRO* 3.7 5.2 - - - +
192A TYR* 3.1 22.4 + - - -
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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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74A ILE* 3.9 23.6 - - + +
77A GLU* 3.4 48.5 - - + +
78A HIS* 3.6 9.2 - - + +
81A ALA* 3.4 33.9 - - + -
102A VAL* 3.1 12.6 + - + +
103A TRP* 3.8 5.6 - - + +
104A LEU 3.1 1.2 - - - -
105A ASP* 1.3 79.5 - - + +
107A ALA* 1.3 65.7 + - - +
108A THR 3.1 1.6 - - - -
109A PRO* 3.1 14.3 - - - +
110A TYR* 3.8 10.7 - - - -
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Residues in contact with ALA 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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74A ILE* 4.3 9.0 - - + -
103A TRP* 2.8 38.9 + - + +
104A LEU* 3.8 3.8 - - + +
106A ILE* 1.3 73.9 - - - +
108A THR* 1.3 54.0 + - - +
109A PRO 3.3 0.2 - - - -
110A TYR* 2.5 43.3 + - + +
180A TRP* 3.5 33.3 - - + -
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Residues in contact with THR 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 LEU 2.7 19.5 + - - -
105A ASP* 3.4 14.6 - - - -
106A ILE 3.1 1.8 - - - -
107A ALA* 1.3 75.5 - - - +
109A PRO* 1.3 68.1 - - + +
110A TYR 3.2 0.5 + - - -
111A HIS* 3.5 14.2 + - - +
180A TRP* 4.1 13.4 + - - -
187A GLY 5.4 4.1 + - - +
188A ARG* 5.5 3.3 + - - +
192A TYR* 3.5 16.5 + - - -
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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