Contacts of the strand formed by residues 77 - 87 (chain B) in PDB entry 4PBY
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 ASN 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B THR* 2.9 18.7 + - - +
72B THR* 2.9 43.3 + - - -
75B GLU 3.7 3.6 + - - -
76B GLN* 1.3 97.5 + - - +
78B HIS* 1.3 68.5 + - - +
123B HIS* 3.0 17.1 + - - +
125B GLY* 3.3 26.8 - - - +
126B GLU* 3.3 30.2 + - - +
127B VAL* 5.3 0.4 - - + +
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Residues in contact with HIS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TRP* 6.2 1.8 - + - -
69B GLY* 3.6 4.7 - - - -
70B THR* 2.9 39.9 + - + +
76B GLN* 3.5 32.0 + - + +
77B ASN* 1.3 78.3 + - - +
79B LEU* 1.3 66.8 + - - +
80B VAL* 3.7 11.0 + - + +
120B LYS* 4.1 25.7 + - + +
121B ILE 3.1 16.0 + - - +
122B ASN* 3.3 25.3 + - - -
123B HIS* 4.1 5.6 - - - -
127B VAL* 3.9 3.6 - - - +
161B PRO* 4.1 16.3 - - + +
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Residues in contact with LEU 79 (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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67B VAL* 4.2 10.1 - - + -
68B LEU 3.6 17.5 - - - +
78B HIS* 1.3 71.8 - - - +
80B VAL* 1.3 61.2 + - - +
81B ILE* 5.9 2.0 - - + -
119B ILE* 4.1 0.7 - - - +
120B LYS* 3.5 2.6 - - - -
121B ILE* 2.7 55.1 + - + +
123B HIS* 3.9 13.1 - - + +
127B VAL* 4.5 9.4 - - + -
130B ALA* 4.0 24.0 - - + -
140B ILE* 4.3 22.7 - - + -
142B THR* 4.3 6.1 - - + -
152B PHE* 3.9 34.8 - - + -
154B TYR* 6.1 0.4 - - + -
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 6.2 1.3 - - + -
67B VAL* 3.7 1.9 - - - +
68B LEU* 2.9 55.0 + - + +
69B GLY* 4.6 4.0 - - - +
70B THR* 4.4 12.1 - - + -
78B HIS* 3.9 20.9 - - + +
79B LEU* 1.3 80.9 - - - +
81B ILE* 1.3 83.2 + - - +
82B ALA 4.3 0.9 - - - +
117B ILE* 4.2 20.2 - - + -
119B ILE* 3.5 8.3 - - - +
120B LYS* 4.4 11.7 - - + -
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Residues in contact with ILE 81 (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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50B LEU* 4.1 22.2 - - + -
65B ARG* 4.2 15.9 - - + +
66B LEU 3.3 9.9 - - - +
67B VAL* 4.7 2.9 - - + -
79B LEU* 5.9 2.7 - - + -
80B VAL* 1.3 84.3 - - - +
82B ALA* 1.3 70.2 + - - +
118B GLU* 3.0 26.0 + - + -
119B ILE* 3.3 31.4 + - + +
121B ILE* 6.3 0.4 - - + -
140B ILE* 4.2 12.8 - - + -
154B TYR* 3.6 52.3 - - + -
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Residues in contact with ALA 82 (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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40B LEU* 6.2 0.7 - - + -
65B ARG* 3.1 10.4 - - - +
66B LEU* 2.8 39.3 + - + +
68B LEU* 4.0 26.2 - - + -
80B VAL* 4.3 3.3 - - + +
81B ILE* 1.3 75.3 - - - +
83B SER* 1.3 63.5 + - - +
84B VAL* 5.1 0.2 - - - -
115B ILE* 4.9 9.2 - - + -
116B GLU 3.3 14.4 - - - +
117B ILE* 4.5 6.1 - - + -
118B GLU* 4.3 2.0 - - - +
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Residues in contact with SER 83 (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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63B ILE* 4.6 13.0 - - - -
64B HIS 3.4 7.6 - - - -
65B ARG* 4.3 2.5 - - - -
82B ALA* 1.3 73.7 - - - +
84B VAL* 1.3 65.4 + - - +
85B GLN* 6.1 1.0 - - - +
114B LYS 4.8 1.9 + - - -
115B ILE* 3.2 8.5 - - - +
116B GLU* 2.7 52.0 + - - +
118B GLU* 3.5 27.0 + - - +
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Residues in contact with VAL 84 (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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36B MET* 4.0 15.0 - - + -
49B TRP* 3.8 22.2 - - + -
62B SER 3.7 0.5 - - - +
63B ILE* 3.7 4.1 - - - -
64B HIS* 2.9 36.7 + - + +
66B LEU* 3.7 30.3 - - + -
82B ALA* 5.0 0.7 - - + +
83B SER* 1.3 80.5 - - - +
85B GLN* 1.3 67.8 + - - +
86B LEU* 3.8 24.5 + - + -
114B LYS 3.8 3.4 - - - -
115B ILE* 4.2 7.6 - - + -
399B MET* 4.2 10.5 - - + -
401B VAL* 4.4 7.2 - - + -
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Residues in contact with GLN 85 (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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36B MET* 3.7 16.3 - - - +
61B PHE* 3.4 45.7 - - + -
62B SER 3.5 3.8 - - - +
63B ILE* 3.8 22.9 - - + +
83B SER* 6.1 1.1 - - - +
84B VAL* 1.3 74.0 - - - +
86B LEU* 1.3 67.9 + - - +
87B PRO* 4.4 1.6 - - - +
112B SER 4.7 0.7 - - - +
113B GLY* 3.7 15.7 - - - -
114B LYS* 3.1 45.9 + - - +
116B GLU* 5.7 1.4 + - - -
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Residues in contact with LEU 86 (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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34B LEU* 3.8 26.2 - - + -
36B MET* 3.9 4.0 - - - -
49B TRP* 4.6 3.8 - - + -
61B PHE* 3.1 6.7 - - - +
62B SER* 2.7 38.3 + - - +
64B HIS* 3.6 33.7 - - + +
84B VAL* 3.9 17.7 - - + -
85B GLN* 1.3 83.3 - - - +
87B PRO* 1.3 71.7 - - + +
383B ASN* 3.9 18.8 - - - +
386B GLU* 4.1 11.7 - - + -
389B VAL* 4.3 14.4 - - + -
401B VAL* 3.9 11.2 - - + -
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Residues in contact with PRO 87 (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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34B LEU* 4.2 26.2 - - + -
36B MET* 5.6 0.9 - - - -
60B ASP* 4.2 10.3 - - - +
61B PHE* 4.4 1.3 - - + -
62B SER* 4.4 2.9 + - - -
85B GLN 4.4 2.5 - - - +
86B LEU* 1.3 97.2 - - + +
88B ASN* 1.3 67.9 + - - +
89B ASP 3.9 0.2 + - - -
91B ALA* 4.4 5.2 - - + -
97B HIS* 3.7 41.5 - - + +
386B GLU* 4.4 9.0 - - - +
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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