Contacts of the strand formed by residues 96 - 105 (chain B) in PDB entry 6UPR
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 GLN 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B GLY* 3.3 15.8 - - - +
43B PHE 3.3 23.7 + - - +
89B ASP* 4.5 9.7 - - - +
90B LEU 3.7 7.8 + - - +
91B GLN* 2.3 35.4 + - - +
94B ASN 4.4 0.2 + - - -
95B VAL* 1.3 70.8 - - - +
97B LEU* 1.3 67.9 + - - +
98B LYS 3.8 0.5 + - - -
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Residues in contact with LEU 97 (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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43B PHE* 3.6 29.2 - - + +
45B PHE* 3.7 26.9 - - + -
65B PHE* 4.3 17.5 - - + -
88B TYR 3.6 1.2 - - - +
89B ASP* 3.5 4.2 - - - -
90B LEU* 2.8 48.5 + - + +
92B GLU* 4.0 25.1 - - + +
95B VAL* 2.9 14.1 + - + +
96B GLN* 1.3 75.7 + - - +
98B LYS* 1.3 60.8 + - - +
99B LEU* 3.5 13.9 - - + +
285B MET* 4.2 18.2 - - + -
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Residues in contact with LYS 98 (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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43B PHE 3.2 9.9 + - - +
44B SER* 3.3 15.1 - - - +
45B PHE 3.0 22.6 + - - +
46B ASN* 4.5 1.0 - - - +
87B THR* 3.8 20.6 - - + -
88B TYR 3.7 2.5 - - - -
89B ASP* 2.7 38.1 + - - +
96B GLN 3.8 0.8 + - - -
97B LEU* 1.3 70.1 - - - +
99B LEU* 1.3 60.8 + - - +
100B THR* 3.7 1.6 + - - -
146B HIS* 3.4 33.6 + - + +
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Residues in contact with LEU 99 (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* 3.3 23.6 - - + +
47B ILE* 3.9 27.1 - - + -
65B PHE* 3.5 34.5 - - + -
69B PHE* 3.9 14.1 - - + -
86B GLN 3.7 0.9 - - - +
87B THR* 3.1 1.6 - - - +
88B TYR* 2.5 48.1 + - + +
90B LEU* 3.9 14.1 - - + -
97B LEU* 3.5 11.8 - - + -
98B LYS* 1.3 72.6 - - - +
100B THR* 1.3 66.3 + - - +
101B ILE* 3.9 23.1 - - + -
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Residues in contact with THR 100 (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 2.9 7.8 + - - +
46B ASN* 3.3 21.7 + - + +
47B ILE* 2.9 28.2 + - - +
85B PRO* 4.0 15.0 - - + -
86B GLN 3.3 9.2 - - - +
87B THR* 2.8 27.3 + - - +
98B LYS 3.7 0.9 + - - -
99B LEU* 1.3 72.6 - - - +
101B ILE* 1.3 64.2 + - - +
102B VAL* 3.7 22.0 - - + -
123B TYR* 4.5 4.5 - - - +
146B HIS* 4.5 10.6 + - - -
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Residues in contact with ILE 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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47B ILE* 3.6 7.9 - - + +
49B CYS* 4.6 10.1 - - + -
61B MET* 4.2 36.1 - - + -
65B PHE* 4.7 1.3 - - + -
69B PHE* 3.7 40.2 - - + -
84B ARG 3.6 2.6 - - - +
85B PRO* 3.5 1.7 - - - +
86B GLN* 2.8 35.7 + - + +
88B TYR* 4.2 8.7 - - + -
99B LEU* 3.9 24.0 - - + -
100B THR* 1.3 74.4 - - - +
102B VAL* 1.3 64.9 + - - +
103B ASP* 4.1 4.8 + - + +
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Residues in contact with VAL 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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47B ILE 2.7 15.5 + - - +
48B LEU* 3.5 7.6 - - + +
49B CYS* 2.7 34.7 + - - +
83B LEU* 3.7 27.6 - - + -
84B ARG 3.6 12.1 - - - +
85B PRO* 3.9 2.9 - - + -
100B THR* 3.7 16.6 - - + +
101B ILE* 1.3 77.2 - - - +
103B ASP* 1.3 58.1 + - - +
123B TYR* 3.6 37.0 - - + +
150B ILE* 3.8 22.0 - - + -
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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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49B CYS* 3.7 8.5 - - + +
57B LYS* 2.6 40.5 + - - +
58B SER* 5.3 1.9 + - - -
74B ALA* 6.2 0.2 - - - +
82B ARG 3.3 0.3 - - - +
83B LEU* 3.5 3.8 - - - -
84B ARG* 2.9 63.3 + - - +
101B ILE* 4.1 5.6 + - + +
102B VAL* 1.3 73.2 - - - +
104B ALA* 1.3 69.7 + - - +
105B VAL* 3.2 16.2 + - + +
401B GTP 4.2 12.1 + - - -
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Residues in contact with ALA 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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48B LEU* 4.8 0.2 - - - +
49B CYS 3.2 15.2 + - - +
50B VAL* 4.4 7.9 - - + -
57B LYS* 3.4 10.9 + - - -
81B VAL* 3.9 17.9 - - + -
82B ARG 3.4 5.2 - - - -
83B LEU* 4.1 9.7 - - + +
102B VAL 4.2 0.2 - - - -
103B ASP* 1.3 78.3 + - - +
105B VAL* 1.3 63.6 + - - +
106B GLY 3.6 0.9 + - - -
107B PHE* 3.7 14.7 + - + +
120B ILE* 4.1 23.8 - - + -
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Residues in contact with VAL 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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57B LYS* 5.0 1.1 - - - +
74B ALA* 4.0 24.0 - - + -
78B GLU* 4.2 19.4 - - + +
80B CYS 3.9 1.6 - - - +
81B VAL* 3.2 8.3 - - - -
82B ARG* 2.5 61.5 + - + +
84B ARG* 3.8 29.2 - - + +
103B ASP* 3.6 25.8 - - - +
104B ALA* 1.3 70.8 - - - +
106B GLY* 1.3 63.7 + - - +
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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