Contacts of the helix formed by residues 91 - 101 (chain A) in PDB entry 3L7N
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 CYS 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLU* 4.9 3.6 - - - -
53A GLY* 3.8 14.6 - - - -
54A GLY 4.1 11.2 - - - -
90A VAL* 1.3 68.5 - - - +
92A LEU* 1.3 77.6 + - - +
94A ALA* 2.7 21.7 + - - +
95A GLN* 3.1 19.0 + - - +
142A TRP 4.6 11.7 - - - +
143A HIS* 5.3 2.5 - - + -
176A PHE 2.9 12.9 + - - -
177A GLN* 3.5 34.1 + - - +
179A HIS* 3.7 22.7 - - + +
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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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8A HIS* 3.9 25.6 - - + +
53A GLY* 3.8 0.4 - - - -
54A GLY* 3.7 22.7 - - - +
56A GLN* 3.5 35.0 - - + +
57A SER 3.8 4.0 - - - -
58A PRO* 3.8 26.0 - - + -
68A TYR* 3.8 25.6 - - + +
90A VAL 2.9 1.4 + - - -
91A CYS* 1.3 82.1 - - - +
93A GLY* 1.3 65.1 + - - +
95A GLN* 3.0 11.4 + - - +
96A LEU* 3.0 33.2 + - + +
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Residues in contact with GLY 93 (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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8A HIS* 5.0 0.2 - - - -
51A LEU* 3.6 27.5 - - - +
52A MET 3.5 8.7 + - - -
89A GLY* 3.5 8.3 - - - -
90A VAL 2.7 17.1 + - - -
92A LEU* 1.3 74.2 - - - +
94A ALA* 1.4 54.0 + - - -
96A LEU* 3.5 9.2 + - - +
97A MET* 3.2 31.5 + - - +
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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
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89A GLY* 3.3 23.0 - - - +
91A CYS* 2.7 16.0 + - - +
93A GLY* 1.4 69.9 - - - +
95A GLN* 1.3 57.2 + - - +
97A MET* 3.5 4.7 + - - +
98A GLY 3.2 19.6 + - - -
147A PRO* 3.5 19.8 - - + +
169A PHE* 4.3 3.6 - - - -
175A ALA* 3.7 17.4 - - + +
176A PHE 3.6 18.4 - - - +
177A GLN* 4.3 3.6 - - - +
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Residues in contact with GLN 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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56A GLN 5.3 0.7 - - - +
57A SER* 5.1 1.9 - - - -
58A PRO* 3.6 30.5 - - + +
91A CYS* 3.7 13.9 + - - +
92A LEU* 3.0 13.5 + - - +
94A ALA* 1.3 75.5 - - - +
96A LEU* 1.3 62.9 + - - +
98A GLY* 3.2 2.4 + - - -
99A VAL* 3.1 26.2 + - - +
103A ALA 5.1 0.2 - - - +
105A TYR* 4.3 8.1 - - + +
143A HIS* 5.1 1.2 - - - +
145A ASP* 3.6 32.3 - - - +
146A MET 3.8 16.4 - - - +
147A PRO* 3.9 6.5 - - - -
177A GLN* 2.8 36.9 + - - +
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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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8A HIS* 4.3 4.5 - - + +
51A LEU* 4.8 3.8 - - + -
58A PRO* 3.9 26.7 - - + -
68A TYR* 4.1 9.2 - - - +
70A ALA* 4.2 11.4 - - + +
73A GLU* 3.7 28.9 - - + +
74A VAL* 3.9 22.1 - - + +
77A ILE* 3.9 17.4 - - + +
92A LEU* 3.0 39.9 + - + +
93A GLY* 4.0 6.7 - - - +
95A GLN* 1.3 71.9 - - - +
97A MET* 1.3 61.8 + - - +
99A VAL* 3.3 5.0 + - - +
100A ALA* 2.8 29.5 + - - +
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Residues in contact with MET 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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51A LEU* 4.8 0.9 - - + -
77A ILE* 4.2 17.0 - - + -
87A ILE* 3.8 28.7 - - + -
89A GLY* 3.4 22.0 - - - -
93A GLY 3.2 12.9 + - - +
94A ALA 3.6 7.4 - - - +
95A GLN 3.3 0.2 - - - -
96A LEU* 1.3 77.4 - - - +
98A GLY* 1.3 63.4 + - - +
100A ALA* 3.0 7.2 + - - -
101A TYR* 3.0 38.0 + - + -
169A PHE* 4.0 25.4 - - + -
173A GLN* 4.2 15.0 - - + -
174A TYR 3.4 25.4 - - - +
175A ALA* 4.2 5.2 - - - -
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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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94A ALA 3.2 12.6 + - - -
95A GLN 3.2 5.2 + - - -
97A MET* 1.3 73.8 - - - +
99A VAL* 1.4 62.4 + - - +
101A TYR* 3.0 12.1 + - - +
102A GLY 3.1 0.9 + - - -
103A ALA* 3.0 28.8 + - - +
147A PRO* 4.8 2.9 - - - -
148A GLY 4.0 10.1 - - - -
150A PRO* 4.3 0.2 - - - +
169A PHE* 3.6 21.5 - - - -
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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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58A PRO* 4.1 18.4 - - + +
71A GLN* 5.6 4.5 - - - +
74A VAL* 3.9 24.9 - - + +
78A GLN* 5.0 0.7 - - - +
95A GLN 3.1 15.0 + - - +
96A LEU 3.8 5.4 - - - +
98A GLY* 1.4 73.2 - - - +
100A ALA* 1.3 65.6 - - - +
101A TYR 3.0 0.9 + - - -
102A GLY* 3.1 13.0 + - - -
103A ALA 3.2 12.9 + - - +
104A ASP* 3.9 24.9 - - + +
105A TYR 4.5 2.0 - - - +
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Residues in contact with ALA 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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74A VAL* 3.7 17.2 - - + +
77A ILE* 3.5 31.6 - - + -
78A GLN* 3.2 31.8 - - + +
96A LEU 2.8 18.4 + - - +
97A MET 3.0 5.3 + - - +
99A VAL* 1.3 76.4 - - - +
101A TYR* 1.3 61.9 + - + +
102A GLY* 3.4 1.3 + - - -
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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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77A ILE* 4.6 11.0 - - + -
81A ALA* 3.2 29.0 - - + +
87A ILE* 5.5 0.2 - - + -
97A MET* 3.0 40.2 + - + +
98A GLY 3.0 4.7 + - - +
100A ALA* 1.3 81.8 - - + +
102A GLY* 1.4 55.2 + - - +
103A ALA 3.6 0.2 - - - -
150A PRO* 3.3 17.1 - - + +
152A LYS* 3.0 37.0 + - + +
169A PHE* 3.6 54.5 + + + -
170A GLY* 4.7 1.4 - - - -
173A GLN* 3.3 22.4 + - + +
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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