Contacts of the strand formed by residues 91 - 98 (chain A) in PDB entry 4N20
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 ASP 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A SER* 3.4 6.5 + - - -
47A HIS* 4.0 20.6 + - - +
48A VAL* 3.8 6.9 - - + +
81A MET* 3.4 28.5 - - + +
85A SER* 2.5 29.8 + - - -
89A SER* 3.3 20.4 + - - -
90A SER* 1.3 73.4 + - - +
92A LYS* 1.3 63.1 + - - +
112A PHE* 3.8 3.8 - - - +
113A LEU* 2.9 42.3 + - + +
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Residues in contact with LYS 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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43A LYS* 6.3 1.2 - - - +
44A HIS* 3.3 7.9 - - - +
45A SER* 3.0 46.4 + - - +
48A VAL* 3.8 4.3 - - - +
90A SER* 4.2 18.2 - - - +
91A ASP* 1.3 77.5 - - - +
93A VAL* 1.3 67.6 + - - +
94A THR* 4.5 14.3 + - - +
111A LEU 3.2 12.3 - - - +
112A PHE* 4.1 29.4 - - + -
113A LEU* 4.6 1.8 - - - +
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Residues in contact with VAL 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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9A LEU* 5.6 1.5 - - + +
42A LEU* 4.6 4.7 - - + -
43A LYS 3.4 11.2 - - - +
44A HIS* 4.1 0.4 - - + -
48A VAL* 3.7 24.7 - - + -
50A VAL* 3.8 18.4 - - + -
77A LEU* 4.2 26.0 - - + -
79A VAL* 4.5 11.9 - - + -
92A LYS* 1.3 79.5 - - - +
94A THR* 1.3 71.4 + - - +
95A VAL* 4.3 4.2 - - + +
109A ALA 4.2 0.5 - - - +
110A GLY* 3.6 1.4 - - - -
111A LEU* 2.8 44.6 + - + +
113A LEU* 4.8 5.4 - - + -
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Residues in contact with THR 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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42A LEU* 3.2 4.7 - - - +
43A LYS* 2.8 47.3 + - + +
92A LYS* 4.5 16.5 + - - +
93A VAL* 1.3 76.3 + - - +
95A VAL* 1.3 68.4 + - - +
96A ASN* 4.1 9.1 + - - +
108A GLN* 3.7 37.0 + - + +
109A ALA 3.8 6.7 - - - +
110A GLY* 4.4 3.7 - - - -
112A PHE* 5.8 2.4 - - - -
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Residues in contact with VAL 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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9A LEU* 3.6 24.7 - - + -
29A VAL* 3.9 14.6 - - + -
40A PHE* 4.0 13.9 - - + -
41A SER 3.4 9.9 - - - +
42A LEU* 4.3 7.2 - - + -
77A LEU* 4.1 14.6 - - + -
93A VAL* 4.6 4.9 - - + -
94A THR* 1.3 78.1 - - - +
96A ASN* 1.3 67.0 + - - +
97A TYR* 3.7 31.3 - - + +
108A GLN* 3.2 5.8 - - - +
109A ALA 2.8 39.1 + - - +
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Residues in contact with ASN 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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40A PHE* 3.1 8.1 - - - +
41A SER* 2.9 49.3 + - - +
42A LEU* 5.5 0.4 - - - +
43A LYS* 5.2 14.3 - - - +
94A THR* 4.7 11.2 + - - +
95A VAL* 1.3 74.1 - - - +
97A TYR* 1.3 61.4 + - - +
98A TYR* 3.6 11.1 + - - +
105A PRO* 3.8 26.2 - - + +
107A ASP 3.6 2.0 - - - -
108A GLN* 3.3 27.7 + - - +
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Residues in contact with TYR 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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9A LEU* 3.9 5.4 - - - +
11A TYR* 4.7 0.9 - - + -
29A VAL* 2.6 35.4 + - - -
32A ALA* 3.4 23.3 - - - +
33A ALA* 3.5 25.4 - - + -
34A PRO* 3.6 24.9 - - + -
37A ALA* 4.2 5.2 - - + -
39A THR 3.6 2.0 - - - +
40A PHE* 4.0 5.8 - - + -
71A LEU* 3.8 18.6 - - + -
95A VAL* 3.7 24.0 - - + +
96A ASN* 1.3 72.8 - - - +
98A TYR* 1.3 58.5 + - - +
105A PRO* 3.2 5.5 - - - +
106A ILE* 2.8 36.2 + - + -
107A ASP* 3.0 23.7 + - + +
108A GLN 4.5 0.9 - - - -
109A ALA* 4.0 18.8 - - + -
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Residues in contact with TYR 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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37A ALA* 3.5 2.1 - - - -
38A GLN 2.7 30.3 + - - -
39A THR* 3.0 40.0 + - - +
41A SER* 2.7 39.2 + - - -
68A ARG* 3.8 19.1 - - - +
96A ASN* 3.6 18.5 + - + +
97A TYR* 1.3 74.0 - - - +
99A ASP* 1.3 59.6 + - - +
102A GLY 4.3 3.8 - - - +
103A SER* 3.2 38.6 - - - -
104A ILE 3.9 2.0 - - - -
105A PRO* 3.6 31.6 - - + +
106A ILE* 4.2 8.5 - - - +
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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