Contacts of the strand formed by residues 73 - 82 (chain A) in PDB entry 2NSQ
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 LYS 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A VAL 3.6 5.4 - - - +
28A SER* 3.8 14.6 - - - -
29A GLY 5.2 0.6 + - - +
64A LYS* 4.9 0.5 + - - -
66A ILE* 3.7 19.3 - - - +
71A ASN* 2.8 31.2 + - - +
72A PRO* 1.3 75.4 - - - +
74A TRP* 1.3 62.6 + - - +
75A ASN* 4.2 14.5 - - - +
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Residues in contact with TRP 74 (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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26A VAL* 3.6 26.2 - - + +
27A VAL 2.8 8.7 + - - -
28A SER* 3.5 17.7 - - - -
29A GLY* 3.3 22.4 - - - -
43A PRO* 3.2 17.1 + - + -
44A TYR* 3.8 13.5 - - - -
45A VAL* 3.4 26.5 - - + -
63A THR* 3.4 14.6 + - - -
64A LYS* 2.9 55.2 + - + +
66A ILE* 3.7 17.1 - - + +
72A PRO* 3.5 28.3 - - + -
73A LYS* 1.3 74.0 - - - +
75A ASN* 1.3 69.6 + - - +
76A GLU* 3.3 9.8 + - + +
93A VAL* 4.4 11.9 - - + -
146A LEU* 3.7 9.0 - - + -
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Residues in contact with ASN 75 (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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25A LYS* 3.5 36.8 + - - +
26A VAL 3.0 6.3 + - - -
27A VAL* 2.9 31.2 + - - +
73A LYS* 4.2 15.9 - - - +
74A TRP* 1.3 77.5 - - - +
76A GLU* 1.3 59.5 + - - +
77A GLU 4.3 0.3 + - - -
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Residues in contact with GLU 76 (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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25A LYS* 3.2 4.9 - - - +
26A VAL* 2.7 36.5 + - - +
62A GLN 4.4 1.4 - - - +
63A THR* 3.3 26.4 - - + -
64A LYS* 2.8 61.9 + - - +
74A TRP* 3.5 5.2 - - + +
75A ASN* 1.3 77.0 - - - +
77A GLU* 1.3 60.7 + - - +
78A PHE* 3.7 22.6 - - + -
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Residues in contact with GLU 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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7A GLU* 4.2 14.6 - - - +
10A TYR* 5.4 0.3 - - - -
23A ARG* 2.6 42.0 + - + +
24A VAL 3.3 7.2 - - - +
25A LYS* 4.2 9.9 - - + +
75A ASN 4.3 0.6 + - - +
76A GLU* 1.3 72.9 - - - +
78A PHE* 1.3 76.9 + - - +
79A TYR* 3.5 32.4 + - + -
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Residues in contact with PHE 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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10A TYR* 3.8 26.2 - + + -
22A LEU 3.8 0.3 - - - +
23A ARG* 3.6 2.9 - - - +
24A VAL* 2.7 38.1 + - + +
26A VAL* 4.0 16.4 - - + -
47A LEU* 3.9 20.2 - - + -
61A VAL* 3.8 32.8 - - + -
62A GLN 4.4 1.6 - - - -
63A THR* 4.0 15.3 - - + -
76A GLU* 3.7 46.2 - - + -
77A GLU* 1.3 79.8 - - - +
79A TYR* 1.3 66.8 + - - +
80A PHE* 3.6 21.3 - - + -
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Residues in contact with TYR 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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7A GLU* 3.7 35.3 - - + +
8A PRO* 3.6 17.0 + - + +
9A VAL* 3.4 14.7 - - + -
10A TYR* 2.8 31.2 + - - -
21A ILE* 3.8 21.8 - - + -
22A LEU 3.3 3.8 - - - +
23A ARG* 3.5 43.9 + - + -
77A GLU* 3.5 29.4 + - + -
78A PHE* 1.3 76.3 - - - +
80A PHE* 1.3 61.8 + - - +
120A PRO* 4.5 7.1 - - - +
153A MET* 4.0 18.8 - - + -
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Residues in contact with PHE 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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9A VAL* 4.0 4.9 - - - -
10A TYR* 3.3 31.4 - + + -
20A ARG 3.5 0.9 - - - +
21A ILE* 3.4 4.9 - - - -
22A LEU* 2.7 39.9 + - + +
24A VAL* 3.9 18.8 - - + -
47A LEU* 3.8 31.0 - - + -
49A LEU* 4.1 27.1 - - + -
59A ALA* 4.4 7.9 - - + -
61A VAL* 4.0 18.2 - - + -
78A PHE* 3.6 20.9 - - + -
79A TYR* 1.3 76.1 - - - +
81A ARG* 1.3 58.3 + - - +
82A VAL* 3.4 19.5 + - + +
89A LEU* 4.1 17.0 - - + -
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Residues in contact with ARG 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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9A VAL* 3.7 36.7 + - + +
10A TYR 2.9 8.9 + - - +
11A GLY* 2.8 43.7 + - - +
12A LEU* 4.4 9.3 - - - +
13A SER* 3.1 41.5 - - - +
16A GLU* 6.3 0.2 - - - +
19A SER* 4.0 12.3 - - - +
20A ARG 3.5 5.8 - - - +
21A ILE* 4.4 13.6 - - + +
49A LEU* 3.4 18.5 - - - +
58A LEU* 5.6 0.2 - - - +
80A PHE* 1.3 69.9 - - - +
82A VAL* 1.3 61.3 + - - +
87A HIS* 4.6 3.1 + - - -
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Residues in contact with VAL 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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18A GLU 3.7 0.2 - - - +
19A SER* 3.1 8.4 - - - -
20A ARG 2.8 40.6 + - - +
22A LEU* 4.2 9.4 - - + -
49A LEU* 3.6 16.6 - - + -
80A PHE* 3.4 27.6 - - + +
81A ARG* 1.3 80.2 - - - +
83A ASN* 1.3 61.0 + - - +
84A PRO* 3.7 1.6 - - - +
87A HIS* 3.7 9.4 - - - +
112A LEU* 3.9 19.5 - - + -
152A TYR* 3.5 39.7 - - + +
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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