Contacts of the helix formed by residues 85 - 98 (chain A) in PDB entry 3L6B
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 GLY 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A SER* 2.8 10.5 + - - -
84A SER* 1.3 82.3 + - - +
86A ASN* 1.3 62.4 + - - +
88A GLY* 3.7 0.5 - - - -
89A GLN* 2.9 31.1 + - - +
106A VAL* 5.4 0.2 - - - -
114A LYS* 3.9 18.9 - - - +
118A ILE* 3.9 18.3 - - - +
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Residues in contact with ASN 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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52A THR* 4.7 1.7 + - - -
54A SER* 3.5 17.6 + - - +
56A LYS* 3.8 4.5 - - + +
84A SER* 4.8 0.8 + - - +
85A GLY* 1.3 73.8 - - - +
87A HIS* 1.3 67.1 + - - +
89A GLN* 3.4 5.8 + - - +
90A ALA* 3.0 23.6 + - - +
114A LYS* 3.4 20.0 - - - +
239A GLY* 5.9 0.4 - - - -
283A GLU* 3.0 27.3 + - - -
316A ASN* 2.8 27.7 + - - +
348A MLI 3.3 11.3 + - - +
350A PLP 2.9 30.5 + - - +
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Residues in contact with HIS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LYS* 3.7 26.6 + - - +
60A ALA* 4.6 13.8 - - + +
81A THR* 3.2 29.3 + - + +
82A HIS 4.3 1.3 - - - -
83A SER* 3.7 0.7 - - - +
86A ASN* 1.3 73.4 - - - +
88A GLY* 1.3 57.7 + - - +
90A ALA* 3.3 0.6 + - - -
91A LEU* 2.8 39.3 + - + +
151A VAL* 3.0 29.4 + - + +
152A HIS 4.0 4.3 - - - -
153A PRO* 3.5 28.4 + - + +
159A VAL* 4.2 17.7 - - + +
163A GLN* 5.2 0.2 + - - -
348A MLI 2.8 26.8 + - - +
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Residues in contact with GLY 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR* 4.4 2.2 - - - -
83A SER* 2.9 14.6 + - - -
85A GLY 3.4 2.9 + - - -
86A ASN 3.2 0.2 - - - -
87A HIS* 1.3 77.6 - - - +
89A GLN* 1.3 57.1 + - - +
92A THR* 2.7 34.8 + - - -
104A ILE* 3.6 34.5 - - - +
118A ILE* 4.0 6.3 - - - -
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Residues in contact with GLN 89 (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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52A THR* 3.1 32.3 + - - +
85A GLY 2.9 18.4 + - - +
86A ASN* 3.7 5.3 - - - +
88A GLY* 1.3 74.2 - - - +
90A ALA* 1.3 58.5 + - - +
92A THR* 3.4 3.3 + - - -
93A TYR* 3.0 30.7 + - - +
114A LYS* 5.5 3.8 - - - +
117A ALA* 3.7 26.4 - - + +
118A ILE* 3.8 7.9 - - + +
121A TYR* 2.8 52.3 + - + -
316A ASN* 3.4 17.0 + - - +
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Residues in contact with ALA 90 (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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52A THR* 3.9 17.0 + - - +
56A LYS* 3.6 35.9 - - + +
57A ILE* 3.6 14.9 - - - +
60A ALA* 3.6 3.8 - - + -
86A ASN 3.0 16.9 + - - +
87A HIS* 3.7 3.4 - - - +
89A GLN* 1.3 77.8 - - - +
91A LEU* 1.3 58.2 + - - +
93A TYR* 3.4 0.9 + - - +
94A ALA* 2.9 30.5 + - - +
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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
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60A ALA* 3.7 11.8 - - + +
64A VAL* 3.8 24.5 - - + -
79A VAL* 3.8 22.4 - - + -
80A VAL 4.1 10.5 - - - +
81A THR* 3.6 33.4 - - + -
87A HIS* 2.8 27.5 + - - +
88A GLY 3.9 2.5 - - - +
90A ALA* 1.3 72.7 - - - +
92A THR* 1.3 58.4 + - - +
94A ALA* 3.4 0.6 + - - +
95A ALA* 2.9 32.7 + - - +
104A ILE* 4.2 7.2 - - + -
151A VAL* 4.0 28.9 - - + -
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Residues in contact with THR 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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88A GLY 2.7 23.3 + - - -
89A GLN* 3.7 4.9 - - - -
91A LEU* 1.3 76.5 - - - +
93A TYR* 1.3 57.4 + - - +
95A ALA* 3.8 1.2 - - - +
96A LYS* 2.9 31.5 + - + +
102A ALA* 3.7 13.8 - - + +
104A ILE* 3.4 10.0 - - - +
118A ILE* 4.4 2.4 - - - +
121A TYR* 3.4 37.2 - - + +
122A GLY 4.4 0.4 - - - -
123A ALA* 3.4 35.5 - - + +
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Residues in contact with TYR 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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22A SER 5.5 1.1 - - - -
51A LYS* 4.0 34.7 + - + +
52A THR* 3.8 14.4 - - + -
57A ILE* 3.6 24.9 - - + -
61A LEU* 5.1 1.8 - - + -
89A GLN 3.0 17.4 + - - +
90A ALA 3.7 2.7 - - - +
92A THR* 1.3 77.1 - - - +
94A ALA* 1.3 61.3 + - - +
96A LYS* 3.2 10.2 + - + +
97A LEU* 3.2 61.8 + - + +
121A TYR* 3.7 31.1 - + + +
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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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57A ILE* 4.5 0.9 - - + -
60A ALA* 3.9 14.8 - - + +
61A LEU* 3.9 30.3 - - + +
64A VAL* 3.9 20.7 - - + +
90A ALA 2.9 17.4 + - - +
91A LEU 3.8 3.1 - - - +
93A TYR* 1.3 79.2 - - - +
95A ALA* 1.3 62.2 + - - +
97A LEU* 3.4 16.9 + - - +
98A GLU* 3.7 12.0 - - - +
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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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64A VAL* 4.2 12.0 - - + +
79A VAL* 3.6 28.0 - - + -
91A LEU 2.9 18.0 + - - +
92A THR* 3.8 4.9 - - - +
94A ALA* 1.3 73.8 - - - +
96A LYS* 1.3 64.4 + - - +
98A GLU* 3.0 9.2 + - - -
99A GLY 3.2 0.2 + - - -
100A ILE* 2.8 45.7 + - + +
102A ALA* 4.7 1.3 - - + -
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Residues in contact with LYS 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 THR* 2.9 18.3 + - + +
93A TYR* 3.5 9.0 - - + +
95A ALA* 1.3 76.4 - - - +
97A LEU* 1.3 62.0 + - + +
99A GLY* 3.0 14.8 + - - +
100A ILE 3.9 6.7 + - - +
120A ALA 5.1 3.4 + - - -
121A TYR* 3.6 38.7 + - + +
122A GLY* 5.8 1.1 - - - -
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Residues in contact with LEU 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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22A SER* 5.8 2.0 - - - +
61A LEU* 4.0 21.3 - - + -
65A ARG* 4.7 10.3 - - - +
93A TYR* 3.2 54.0 + - + +
94A ALA 3.5 7.6 - - - +
95A ALA 3.2 0.4 - - - -
96A LYS* 1.3 76.9 - - + +
98A GLU* 1.3 68.6 + - - +
99A GLY 3.8 0.3 + - - -
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Residues in contact with GLU 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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64A VAL* 3.7 19.0 - - + +
65A ARG* 4.2 24.2 + - - +
68A VAL* 4.9 14.2 - - + +
75A LYS* 2.7 44.2 + - - +
94A ALA 3.7 13.3 - - - +
95A ALA 3.0 6.9 + - - +
97A LEU* 1.3 86.1 - - - +
99A GLY* 1.3 62.7 + - - +
100A ILE* 3.5 15.3 + - + +
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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