Contacts of the strand formed by residues 79 - 93 (chain A) in PDB entry 4N1D
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 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A CYS* 3.6 4.5 - - - -
77A SER 4.9 1.8 - - - +
78A THR* 1.3 75.8 - - - +
80A CYS* 1.3 73.9 + - - +
81A VAL* 3.3 17.9 + - + +
113A GLY 3.3 2.9 - - - +
115A ARG 2.9 33.1 + - - +
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Residues in contact with CYS 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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14A CYS* 2.0 51.6 - - + -
15A LYS 3.8 2.5 - - - -
43A CYS* 3.8 18.2 - - - +
44A GLU* 3.6 24.4 - - - -
45A GLY 3.3 22.4 + - - +
47A CYS* 3.5 5.2 - - - -
79A CYS* 1.3 77.6 - - - +
81A VAL* 1.3 65.4 + - - +
82A PRO* 4.9 0.2 - - - +
113A GLY 3.4 5.2 - - - -
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Residues in contact with VAL 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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43A CYS* 3.5 5.8 - - - -
79A CYS* 3.7 23.6 - - + +
80A CYS* 1.3 79.9 - - - +
82A PRO* 1.3 84.2 - - + +
83A THR* 3.7 0.3 - - - +
112A CYS* 3.4 2.1 - - - -
113A GLY 2.9 26.9 + - - +
115A ARG* 3.7 34.1 - - + -
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Residues in contact with PRO 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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43A CYS* 3.4 14.1 - - + +
81A VAL* 1.3 96.9 - - + +
83A THR* 1.3 61.6 + - - +
85A LEU* 3.9 26.9 - - + +
109A VAL* 3.6 33.4 - - + -
111A GLY 3.4 7.9 - - - +
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Residues in contact with THR 83 (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 HIS* 5.7 2.8 + - - +
81A VAL 3.7 2.5 - - - +
82A PRO* 1.3 77.6 - - - +
84A GLU* 1.3 85.9 + - - +
85A LEU* 4.8 3.4 - - - -
111A GLY 2.8 9.1 + - - -
112A CYS 3.5 11.6 + - - -
113A GLY* 3.5 20.4 - - - +
115A ARG* 3.4 48.0 - - + +
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Residues in contact with GLU 84 (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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83A THR* 1.3 107.6 + - - +
85A LEU* 1.3 68.8 + - - +
109A VAL* 3.8 0.5 - - - -
110A GLU* 2.8 31.6 + - + -
111A GLY* 3.2 24.5 + - - +
112A CYS 5.4 0.2 - - - +
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Residues in contact with LEU 85 (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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82A PRO* 3.9 34.1 - - + +
83A THR 4.8 0.9 - - - -
84A GLU* 1.3 84.2 - - - +
86A SER* 1.3 61.9 + - - +
106A ASP* 3.7 51.0 + - + +
107A MET 5.1 0.7 - - - -
108A VAL 3.1 12.6 - - - +
109A VAL* 4.0 15.0 - - + -
110A GLU* 4.2 3.1 - - - +
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Residues in contact with SER 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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85A LEU* 1.3 75.2 - - - +
87A ALA* 1.3 66.4 + - - +
105A GLN* 5.6 0.4 - - - -
106A ASP 4.1 4.0 - - - -
107A MET 2.9 22.8 + - - -
108A VAL* 2.9 27.3 + - - +
110A GLU* 2.9 31.5 + - - +
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Residues in contact with ALA 87 (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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86A SER* 1.3 81.5 + - - +
88A ILE* 1.3 70.3 + - - +
103A ASN* 4.8 6.3 - - + -
104A TYR 3.1 20.0 - - - +
105A GLN* 3.8 29.5 + - - +
108A VAL* 4.8 0.2 - - - +
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Residues in contact with ILE 88 (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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35A PRO* 3.9 22.9 - - + -
38A TYR* 4.0 19.5 - - + -
87A ALA* 1.3 80.8 - - - +
89A SER* 1.3 62.6 + - - +
90A MET* 3.7 27.7 + - + -
103A ASN* 4.4 3.4 - - - -
104A TYR* 2.8 29.9 + - - +
107A MET* 3.9 26.6 - - + +
108A VAL* 3.5 27.8 - - + -
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Residues in contact with SER 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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34A TYR* 4.2 5.5 - - - +
35A PRO* 3.7 12.0 - - - +
88A ILE* 1.3 75.5 - - - +
90A MET* 1.3 65.9 + - - +
101A LEU* 4.4 14.6 - - - -
102A LYS 3.4 7.0 - - - -
103A ASN* 2.6 22.5 + - - -
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Residues in contact with MET 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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23A PHE* 3.8 31.4 - - + -
28A TRP* 6.0 2.2 - - + -
31A TRP* 4.9 5.8 - - + -
32A ILE* 4.3 22.9 - - + -
34A TYR 3.3 5.6 - - - +
35A PRO* 3.8 6.1 - - + -
88A ILE* 3.7 22.2 - - + -
89A SER* 1.3 79.8 - - - +
91A LEU* 1.3 62.8 + - - +
92A TYR* 4.0 6.9 - - + -
100A VAL 3.6 1.6 - - - +
101A LEU* 3.5 5.8 - - - -
102A LYS 2.8 34.3 + - - -
104A TYR* 3.6 46.9 - - + +
107A MET* 4.0 10.3 - - + -
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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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32A ILE* 3.8 1.9 - - - +
33A ILE* 2.8 48.9 + - + -
34A TYR* 2.7 29.8 + - + +
90A MET* 1.3 71.2 - - - +
92A TYR* 1.3 63.0 + - - +
99A VAL* 3.7 23.3 - - + -
100A VAL 3.4 13.2 - - - +
101A LEU* 4.0 25.1 - - + -
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Residues in contact with TYR 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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31A TRP* 3.2 37.5 - + + +
32A ILE* 4.0 5.4 - - + -
33A ILE* 4.0 5.4 - - - +
90A MET* 4.0 11.2 - - + -
91A LEU* 1.3 76.3 - - - +
93A LEU* 1.3 74.4 + - - +
94A ASP* 4.2 13.3 - - + +
98A LYS 3.5 0.2 - - - +
99A VAL* 3.5 4.5 - - - +
100A VAL* 2.7 82.9 + - + +
102A LYS* 4.1 14.6 - - + +
104A TYR* 3.2 36.1 + + - -
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Residues in contact with LEU 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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30A SER 4.3 15.3 - - - +
31A TRP* 2.8 32.8 + - + +
33A ILE* 3.8 20.9 - - + -
92A TYR* 1.3 81.4 - - - +
94A ASP* 1.3 63.1 + - - +
97A GLU* 3.7 49.6 - - + +
98A LYS 3.4 1.1 - - - -
99A VAL* 3.9 22.2 - - + -
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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