Contacts of the strand formed by residues 67 - 78 (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 TRP 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B LEU* 3.2 32.8 + - + -
64B LEU* 2.8 55.1 + - + +
65B ASN 3.4 0.6 + - - -
66B ASN* 1.3 81.7 - - + +
68B ASP* 1.3 86.1 + - - +
69B VAL* 4.3 9.0 - - + +
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Residues in contact with ASP 68 (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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60B ARG* 3.5 38.0 + - + -
61B VAL 3.4 9.0 - - - +
62B ARG* 3.9 9.0 - - - +
63B LEU* 4.7 1.8 - - - -
64B LEU 3.8 7.3 - - - +
65B ASN 5.1 3.3 - - - +
66B ASN 5.7 0.7 - - - -
67B TRP* 1.3 93.9 + - - +
69B VAL* 1.3 70.6 + - - +
173B TYR* 3.3 29.8 + - + +
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG* 3.8 1.5 - - - -
61B VAL* 3.0 33.6 + - + +
63B LEU* 4.0 26.0 - - + +
67B TRP* 4.3 13.2 - - + +
68B ASP* 1.3 81.2 - - - +
70B CYS* 1.3 76.1 + - - +
71B ALA* 3.2 10.6 + - + +
173B TYR* 6.3 0.4 - - - -
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Residues in contact with CYS 70 (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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58B LYS* 6.2 0.2 - - + -
59B GLY 3.5 6.3 - - - +
60B ARG* 4.6 0.9 - - - +
69B VAL* 1.3 77.7 - - - +
71B ALA* 1.3 62.8 + - - +
72B ASP* 3.4 14.2 + - - +
173B TYR* 3.5 18.8 - - - -
174B CYS* 2.0 57.2 - - + -
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Residues in contact with ALA 71 (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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37B LEU* 4.6 5.1 - - + +
57B ALA 3.6 2.1 - - - +
58B LYS* 3.6 4.0 - - - -
59B GLY 2.9 27.1 + - - +
61B VAL* 3.3 28.7 - - + -
69B VAL* 3.2 9.5 + - + +
70B CYS* 1.3 69.6 - - - +
72B ASP* 1.3 64.0 + - - +
73B MET* 4.1 13.8 - - + +
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Residues in contact with ASP 72 (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 ALA 3.8 2.9 - - - -
58B LYS* 3.3 40.6 + - + +
70B CYS* 3.4 12.2 + - - +
71B ALA* 1.3 73.1 - - - +
73B MET* 1.3 61.1 + - - +
92B GLY* 3.6 4.5 - - - -
93B VAL* 3.2 47.0 + - + +
174B CYS* 6.0 0.5 - - - +
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Residues in contact with MET 73 (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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37B LEU* 3.4 35.0 - - + -
56B THR* 3.3 8.1 - - - -
57B ALA* 2.7 32.1 + - + +
58B LYS* 5.3 0.4 - - - +
71B ALA* 4.1 15.5 - - + +
72B ASP* 1.3 79.1 - - - +
74B VAL* 1.3 68.4 + - - +
90B TYR* 4.8 6.1 - - - -
91B TRP 3.3 17.9 - - - +
92B GLY* 4.3 5.4 - - - -
93B VAL* 5.3 0.2 - - - +
201B 2WL 3.5 68.9 - - + -
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Residues in contact with VAL 74 (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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54B SER* 6.1 0.4 - - - -
55B ALA 3.5 9.2 - - - +
56B THR* 4.5 13.5 - - + -
73B MET* 1.3 79.5 - - - +
75B GLY* 1.3 65.9 + - - +
76B THR* 4.8 3.1 - - + -
90B TYR* 3.2 5.4 - - - +
91B TRP* 2.8 71.4 + - + +
93B VAL* 3.8 24.5 - - + -
201B 2WL 3.9 5.0 - - - -
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Residues in contact with GLY 75 (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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54B SER* 3.3 5.9 - - - -
55B ALA 2.6 38.6 + - - +
74B VAL* 1.3 77.8 - - - +
76B THR* 1.3 66.6 + - - +
77B PHE* 4.7 3.8 - - - -
88B MET* 4.3 5.6 - - - -
89B LYS 3.4 8.5 - - - -
90B TYR* 4.2 2.5 - - - -
91B TRP* 4.9 0.2 - - - -
201B 2WL 3.9 13.2 - - - -
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Residues in contact with THR 76 (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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53B MET 4.1 4.9 - - - -
54B SER* 4.3 11.0 - - - +
74B VAL* 4.8 3.4 - - + -
75B GLY* 1.3 79.3 - - - +
77B PHE* 1.3 64.9 + - - +
78B THR* 5.2 0.5 + - - -
87B LYS 3.5 1.6 - - - +
88B MET* 3.6 0.6 - - - +
89B LYS* 2.9 56.4 + - - +
91B TRP* 3.7 21.2 - - + -
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Residues in contact with PHE 77 (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* 3.7 25.4 - + - -
52B GLN* 4.4 13.9 - - - +
53B MET* 3.1 48.5 + - + +
54B SER* 3.7 7.2 - - - -
55B ALA* 3.7 27.1 - - + -
75B GLY 4.5 2.7 - - - -
76B THR* 1.3 74.7 - - - +
78B THR* 1.3 61.5 + - - +
79B ASP* 4.3 4.0 + - - +
86B PHE* 3.9 33.0 - + + -
87B LYS 3.4 2.5 - - - -
88B MET* 3.4 41.3 - - + -
104B HIS* 3.4 27.4 - + - -
201B 2WL 4.8 0.9 - + - -
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Residues in contact with THR 78 (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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52B GLN* 5.5 2.6 + - - -
76B THR 5.2 0.7 + - - -
77B PHE* 1.3 75.6 + - - +
79B ASP* 1.3 75.4 + - - +
80B THR* 4.0 2.1 - - + +
86B PHE* 3.4 6.9 - - - -
87B LYS* 2.9 44.7 + - + -
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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