Contacts of the strand formed by residues 70 - 79 (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 ILE 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TRP* 3.6 35.7 - - + +
64A ARG 3.0 4.7 - - - +
65A ASN* 4.6 14.4 - - - +
68A GLY 5.8 0.4 - - - -
69A THR* 1.3 74.7 - - - +
71A GLU* 1.3 63.7 + - - +
72A LEU* 4.0 3.0 + - + +
113A PHE* 3.9 24.2 - - + -
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Residues in contact with GLU 71 (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* 3.1 4.7 - - - -
64A ARG* 2.8 53.5 + - + +
69A THR* 3.8 2.2 + - - +
70A ILE* 1.3 73.7 - - - +
72A LEU* 1.3 68.8 + - - +
73A VAL* 3.7 2.4 - - - +
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Residues in contact with LEU 72 (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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32A TYR* 3.5 46.4 - - + +
34A ALA* 3.7 13.2 - - - +
62A SER 3.4 19.5 - - - +
63A TRP* 4.1 7.9 - - + -
64A ARG* 5.4 1.2 + - - -
70A ILE* 4.0 4.1 + - + +
71A GLU* 1.3 81.4 - - - +
73A VAL* 1.3 61.7 + - - +
74A LYS 4.4 1.6 - - - +
75A LYS* 3.8 38.6 - - + +
113A PHE* 4.5 12.1 - - + -
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Residues in contact with VAL 73 (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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32A TYR* 3.7 2.8 - - - -
34A ALA* 2.9 36.0 + - + +
62A SER* 3.1 17.5 + - - +
63A TRP* 3.6 26.0 - - - +
64A ARG* 4.2 21.8 - - + +
71A GLU 3.7 2.9 - - - +
72A LEU* 1.3 79.5 - - - +
74A LYS* 1.3 80.1 + - + +
99A VAL* 4.9 1.6 - - + -
100B ILE* 3.7 35.4 - - + -
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Residues in contact with LYS 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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31A TYR* 5.6 3.2 + - - -
32A TYR* 3.3 10.5 - - - +
33A ASN* 3.1 29.3 + - - +
35A ASN* 5.9 1.6 - - - -
39A GLU* 3.7 20.3 + - - -
60A TYR* 3.3 22.8 - - + +
61A ALA* 3.6 0.3 - - - -
62A SER* 2.9 35.1 + - - +
72A LEU* 4.4 1.3 - - - +
73A VAL* 1.3 99.2 - - + +
75A LYS* 1.3 65.8 + - - +
92B LEU* 4.3 7.9 - - + -
100B ILE* 4.4 16.8 + - + +
101B ILE* 4.8 1.8 - - - +
102B LYS* 4.2 26.3 + - + +
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Residues in contact with LYS 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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30A ILE* 3.5 28.0 - - + +
31A TYR* 3.3 11.6 - - - -
32A TYR* 2.9 37.5 + - + +
60A TYR* 3.6 26.2 + - - +
61A ALA* 3.8 6.3 - - + -
72A LEU* 3.8 29.7 - - + +
74A LYS* 1.3 79.7 - - - +
76A GLY* 1.3 59.3 + - - +
110A ASN* 3.0 26.9 + - - +
111A GLU* 3.5 25.9 + - - +
113A PHE* 3.8 18.8 - - - -
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Residues in contact with GLY 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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29A CYS* 4.3 7.6 - - - -
30A ILE 3.3 13.6 + - - -
31A TYR* 4.3 2.0 - - - -
47A GLU* 3.3 12.1 - - - -
59A CYS* 3.5 0.7 - - - -
60A TYR* 2.8 43.0 + - - -
75A LYS* 1.3 76.6 - - - +
77A CYS* 1.3 63.3 + - - -
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Residues in contact with CYS 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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29A CYS* 4.2 4.7 - - - +
47A GLU* 2.9 35.8 + - - +
48A ARG 3.8 4.5 - - - -
49A CYS* 2.0 64.4 - - + -
50A GLU 5.4 0.4 - - - +
58A HIS 3.6 4.5 - - - -
59A CYS* 3.9 1.6 - - - -
60A TYR* 3.6 4.0 - - - -
76A GLY* 1.3 75.5 - - - +
78A TRP* 1.3 59.2 + - - +
79A LEU* 6.4 1.8 - - + -
102B LYS* 3.3 21.7 + - - -
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Residues in contact with TRP 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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57A LEU* 4.0 1.9 - - - +
58A HIS* 2.7 46.3 + + - +
59A CYS* 4.2 11.4 - - - +
60A TYR* 3.8 22.0 - + + -
77A CYS* 1.3 74.2 - - - +
79A LEU* 1.3 83.0 + - - +
81A ASP* 3.1 31.8 + - + +
84A CYS* 3.9 0.9 - - - -
101A PHE* 3.7 32.1 - + - -
103A CYS* 3.6 21.4 - - - -
31B ALA* 3.7 20.6 - - + -
32B PRO* 4.1 9.0 - - + -
90B SER* 3.6 36.5 - - - -
91B MET 4.1 3.4 - - - -
92B LEU* 3.9 7.0 - - + -
102B LYS* 4.0 22.9 - - + -
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Residues in contact with LEU 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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50A GLU* 4.2 26.9 - - + +
52A GLU* 6.0 4.3 - - + +
56A ARG 4.9 0.7 - - - -
57A LEU* 4.6 10.1 - - + -
58A HIS* 3.9 0.4 - - - -
77A CYS* 6.3 2.0 - - + -
78A TRP* 1.3 88.6 + - - +
80A ASP* 1.3 72.0 + - + +
81A ASP* 3.0 4.0 + - - +
88B PRO* 3.5 44.4 - - + +
89B MET* 5.4 0.2 - - - -
90B SER* 3.1 27.0 + - - +
104B ASP* 3.6 29.4 - - + +
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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