Contacts of the strand formed by residues 57 - 65 (chain A) in PDB entry 1NYU
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 LEU 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ARG* 4.1 24.8 - - + +
49A CYS* 3.9 25.6 - - + +
50A GLU 4.0 10.5 - - - +
51A GLY* 3.6 27.4 - - - +
52A GLU 5.2 2.0 - - - +
55A LYS* 3.6 12.3 + - + +
56A ARG* 1.3 85.6 - - - +
58A HIS* 1.3 70.2 + - - +
78A TRP 4.3 0.9 - - - +
79A LEU* 4.6 17.3 - - + -
80A ASP 4.7 2.0 - - - +
105A GLU* 3.6 15.0 + - - +
106A GLY 4.8 1.9 + - - -
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Residues in contact with HIS 58 (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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49A CYS* 4.0 4.0 - - - -
56A ARG* 3.5 28.5 - - + -
57A LEU* 1.3 84.9 + - - +
59A CYS* 1.3 72.3 + - - +
77A CYS* 3.5 1.0 - - - -
78A TRP* 2.7 37.7 + + + +
79A LEU 3.6 11.9 - - - -
80A ASP* 3.2 7.3 + - - -
81A ASP 2.8 35.7 + - - -
84A CYS* 3.4 26.6 - - + +
85A TYR* 3.9 14.6 - + - -
103A CYS* 4.5 3.4 - - - -
104A CYS 2.8 16.4 - - - +
105A GLU* 3.7 16.3 - - - +
106A GLY 5.4 0.4 - - - +
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Residues in contact with CYS 59 (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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27A ARG* 6.1 0.7 - - - -
29A CYS* 2.0 53.8 - - + -
49A CYS* 3.8 11.7 - - - -
57A LEU 5.7 0.2 - - - -
58A HIS* 1.3 88.7 - - - +
60A TYR* 1.3 61.7 - - - +
76A GLY 3.5 3.6 - - - +
77A CYS* 3.9 3.1 - - - -
78A TRP* 4.0 4.0 - - - +
103A CYS* 3.8 2.6 - - - -
104A CYS* 2.9 33.5 + - - +
106A GLY 5.4 1.3 - - - -
109A CYS* 4.2 10.7 - - - -
110A ASN* 3.8 11.7 - - - +
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Residues in contact with TYR 60 (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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31A TYR* 5.8 1.4 - - - -
59A CYS* 1.3 75.2 - - - +
61A ALA* 1.3 77.0 + - - +
62A SER* 3.8 17.7 - - - -
74A LYS* 3.3 26.8 - - + +
75A LYS* 3.6 9.7 + - - -
76A GLY* 2.8 50.1 + - - -
77A CYS 3.6 15.9 - - - -
78A TRP* 3.8 16.8 - + + -
90A CYS* 4.7 0.7 - - - -
101A PHE* 3.7 31.4 - + + -
102A CYS 3.6 6.3 - - - +
110A ASN* 2.7 31.3 + - - +
92B LEU* 4.4 5.8 - - + -
102B LYS* 3.1 40.3 - - + +
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Residues in contact with ALA 61 (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 TYR* 1.3 80.6 - - - +
62A SER* 1.3 60.7 + - - +
63A TRP* 3.6 11.2 - - + -
74A LYS 3.6 8.3 - - - -
75A LYS* 3.8 21.3 - - + -
90A CYS* 4.2 2.7 - - - -
101A PHE* 3.3 5.7 - - - -
102A CYS* 3.2 46.1 + - - +
110A ASN* 4.3 4.7 - - + +
113A PHE* 4.3 6.5 - - + -
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Residues in contact with SER 62 (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 TYR* 3.8 5.4 - - - -
61A ALA* 1.3 74.7 - - - +
63A TRP* 1.3 65.8 + - - +
72A LEU* 3.4 8.0 - - - +
73A VAL* 3.1 30.3 + - - +
74A LYS* 2.9 33.7 + - - +
99A VAL* 4.3 3.8 - - - -
100A TYR 3.2 14.1 - - - -
101A PHE* 4.7 1.1 - - - -
92B LEU* 3.8 24.6 - - - +
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Residues in contact with TRP 63 (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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61A ALA* 3.6 17.7 - - + -
62A SER* 1.3 86.7 - - - +
64A ARG* 1.3 91.5 + - - +
65A ASN* 4.2 4.6 - - - +
70A ILE* 3.6 27.4 - - + +
71A GLU 3.1 18.6 - - - +
72A LEU* 4.1 6.7 - - + -
73A VAL* 3.6 4.4 - - - +
92A ALA* 3.8 12.1 - - + -
99A VAL* 3.4 4.9 - - - +
100A TYR* 2.9 62.6 + + + +
102A CYS* 3.7 17.0 - - - -
113A PHE* 3.4 42.5 - + + -
114A THR 3.6 26.7 - - - -
115A HIS* 5.0 1.8 - - + +
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Residues in contact with ARG 64 (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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63A TRP* 1.3 90.0 - - - +
65A ASN* 1.3 59.0 + - - +
66A SER* 3.5 14.1 - - - +
69A THR 3.0 2.1 - - - +
70A ILE* 3.0 9.0 - - - -
71A GLU* 2.8 47.5 + - + +
72A LEU 5.4 1.0 + - - -
73A VAL* 4.2 15.4 - - + +
98A GLN* 3.7 18.2 + - - +
99A VAL* 4.2 11.3 - - + +
100A TYR* 4.4 1.3 - - - -
94B TYR* 5.2 4.6 + - - -
98B GLN 5.9 0.4 + - - -
100B ILE* 3.8 27.5 - - - +
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Residues in contact with ASN 65 (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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63A TRP* 4.9 5.0 - - + +
64A ARG* 1.3 70.3 - - - +
66A SER* 1.3 60.4 + - - +
67A SER 5.0 0.9 - - - -
68A GLY* 3.9 20.8 - - - -
69A THR 3.5 7.5 + - - +
70A ILE* 4.6 11.9 - - - +
98A GLN 5.0 0.8 + - - -
100A TYR* 3.5 44.2 + - + +
115A HIS* 5.2 7.9 - - - +
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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