Contacts of the strand formed by residues 100 - 109 (chain B) in PDB entry 4PSQ
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 GLY 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B LYS* 3.4 7.8 - - - +
90B TYR* 2.7 54.0 + - - -
99B LYS* 1.3 75.0 - - - +
101B ASN* 1.3 61.0 + - - +
201B 2WL 3.5 13.8 - - - -
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Residues in contact with ASN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LYS* 4.1 28.7 + - - +
88B MET 3.3 16.4 + - - +
89B LYS* 3.7 20.9 - - + +
90B TYR* 3.4 3.6 + - - -
100B GLY* 1.3 73.9 - - - +
102B ASP* 1.3 67.6 + - - +
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Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LYS* 3.5 8.1 - - - +
88B MET* 2.7 46.8 + - + +
90B TYR* 3.4 20.0 + - + -
101B ASN* 1.3 79.9 + - - +
103B ASP* 1.3 71.2 + - - +
119B SER* 3.8 6.3 - - - +
121B ARG* 3.0 44.9 + - - +
133B TYR* 2.9 23.5 + - - +
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Residues in contact with ASP 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 6.0 0.2 - - - +
86B PHE 3.7 5.4 - - - +
87B LYS* 2.8 34.4 + - - +
102B ASP* 1.3 78.4 - - - +
104B HIS* 1.3 60.7 + - - +
105B TRP* 4.0 28.8 + - + +
119B SER* 2.6 34.4 + - - +
120B CYS* 3.6 18.7 + - - +
121B ARG* 6.2 0.2 - - - +
133B TYR* 4.5 1.4 + - - -
206B EDO 3.5 27.7 + - - -
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Residues in contact with HIS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B PHE* 3.9 17.8 - + - -
53B MET* 5.3 1.1 - - + -
77B PHE* 3.4 42.0 - + + -
86B PHE* 2.9 44.1 + + + +
88B MET* 3.7 21.6 - - + +
103B ASP* 1.3 75.1 + - - +
105B TRP* 1.3 61.0 + - - +
106B ILE* 3.7 28.9 - - + +
117B GLN* 3.6 28.1 + - + +
118B TYR 3.9 2.7 - - - -
137B PHE* 5.6 1.1 - + - -
201B 2WL 4.0 17.5 - - + -
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Residues in contact with TRP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 3.4 46.7 - - + -
9B PHE* 4.1 16.4 - + + -
11B VAL* 4.0 16.2 - - + -
84B ALA 3.5 3.8 - - - -
85B LYS* 3.5 56.9 - - + +
86B PHE 4.4 2.5 + - - -
103B ASP* 4.0 26.9 - - + +
104B HIS* 1.3 87.7 - - - +
106B ILE* 1.3 62.2 + - - +
107B VAL* 3.3 5.6 + - + -
117B GLN* 3.4 4.9 - - - +
118B TYR* 3.0 58.5 + + + +
120B CYS* 6.2 0.7 - - + -
159B LEU* 6.2 0.2 - - + -
204B EDO 3.7 19.2 + - - -
206B EDO 5.9 0.4 - - - -
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Residues in contact with ILE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 3.6 6.1 - - - +
12B LYS* 2.9 25.7 + - + +
15B PHE* 3.7 45.8 - - + -
20B PHE* 3.8 27.4 - - + -
45B PHE* 5.3 0.7 - - + -
53B MET* 5.5 1.1 - - + -
84B ALA* 3.0 16.2 + - + +
86B PHE* 4.6 3.4 - - + -
104B HIS* 3.7 29.6 + - + +
105B TRP* 1.3 69.7 - - - +
107B VAL* 1.3 59.2 + - - +
108B ASP 4.1 8.1 - - - +
109B THR* 4.0 19.7 - - + -
115B ALA* 5.3 0.9 - - + -
116B VAL 3.9 3.8 - - - +
117B GLN* 4.7 8.7 - - + -
137B PHE* 6.2 0.4 - - + -
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PHE* 6.5 0.2 - - + -
10B ARG 3.8 5.5 - - - +
11B VAL* 3.3 15.7 - - + +
12B LYS* 3.1 15.0 + - - -
105B TRP* 4.0 8.1 - - + +
106B ILE* 1.3 71.7 - - - +
108B ASP* 1.3 62.5 + - - +
116B VAL* 2.8 20.1 + - + +
117B GLN 4.2 1.1 - - - -
118B TYR* 3.4 33.7 - - + +
155B ARG* 4.2 14.3 + - + -
159B LEU* 4.1 21.8 - - + -
203B EDO 3.1 34.2 + - - +
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Residues in contact with ASP 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LYS* 3.9 17.4 + - - +
106B ILE* 3.4 3.2 - - - +
107B VAL* 1.3 81.8 - - + +
109B THR* 1.3 84.8 + - - +
114B TYR* 3.1 23.4 + - + +
115B ALA* 3.5 0.9 - - - +
116B VAL* 2.9 29.6 + - + +
151B ILE* 3.9 0.9 - - - +
155B ARG* 2.8 41.2 + - + +
210B EDO 2.8 25.8 + - - -
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Residues in contact with THR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LYS* 3.0 34.0 + - + +
15B PHE* 4.4 0.2 - - + -
20B PHE* 3.9 6.9 - - + -
24B TRP* 3.9 2.6 - - - -
106B ILE* 4.0 16.4 - - + -
108B ASP* 1.3 84.2 + - - +
110B ASP* 1.3 62.6 + - - +
111B TYR* 3.0 42.1 + - + -
114B TYR* 2.7 34.9 + - - -
115B ALA* 3.6 11.6 - - - +
210B EDO 3.6 3.3 + - - -
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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