Contacts of the strand formed by residues 76 - 86 (chain J) in PDB entry 2QC8
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 76 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317F ALA* 3.3 15.8 - - - +
319F ARG* 2.9 17.0 + - - +
324F ARG* 3.1 31.4 + - - -
326F PRO* 3.8 1.4 - - - +
327F ARG* 3.0 60.7 + - + +
61J ASN* 4.1 17.1 + - + +
62J PHE 3.4 8.1 - - - -
74J ASN 4.5 0.9 - - - +
75J SER* 1.3 76.7 + - - +
77J MET* 1.3 63.0 + - - +
104J TYR* 4.5 5.2 - - - +
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Residues in contact with MET 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61J ASN* 2.9 26.8 - - - -
62J PHE* 2.9 33.3 + - + +
64J GLY* 3.6 13.5 - - - -
69J GLN* 3.5 42.4 - - + +
70J SER* 3.9 6.5 - - - +
75J SER 3.5 11.0 - - - +
76J ASP* 1.3 80.9 - - - +
78J TYR* 1.3 64.3 + - - +
101J VAL* 3.7 14.1 - - + -
102J PHE 3.5 19.7 - - - +
103J LYS* 3.7 25.1 - - + -
104J TYR 5.1 1.3 - - - +
109J ALA* 4.3 3.8 - - + -
110J GLU* 5.8 0.4 - - - +
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Residues in contact with TYR 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327F ARG* 3.4 33.9 - - + -
328F THR* 5.7 6.5 - - - -
331F GLN* 3.7 23.5 + - + +
59J GLU* 4.3 15.0 - - + -
60J TRP 3.6 9.9 - - - -
61J ASN* 4.3 2.9 - - + -
62J PHE* 4.0 2.8 - - - -
77J MET* 1.3 74.1 - - - +
79J LEU* 1.3 63.4 + - - +
80J VAL* 4.2 3.8 - - + -
100J GLU 4.3 0.2 - - - -
101J VAL* 3.4 7.8 - - - -
102J PHE* 3.1 45.3 + - + +
103J LYS 3.2 27.1 - - - -
104J TYR* 3.8 3.9 + - - -
106J ARG* 3.7 48.8 + - + +
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Residues in contact with LEU 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J TYR* 4.3 15.3 - - + -
32J TRP* 3.7 48.7 - - + -
43J LYS* 4.6 0.7 - - - -
59J GLU* 3.4 9.8 - - - +
60J TRP* 2.9 41.5 + - + +
61J ASN* 3.8 24.0 - - - +
62J PHE* 3.7 24.9 - - + -
78J TYR* 1.3 72.9 - - - +
80J VAL* 1.3 61.4 + - - +
81J PRO* 3.7 2.9 - - - +
99J CYS* 3.7 26.5 - - + -
100J GLU 3.6 3.6 - - - +
101J VAL* 4.6 1.3 - - + -
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Residues in contact with VAL 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59J GLU* 4.0 24.2 - - + +
78J TYR* 5.1 4.0 - - + -
79J LEU* 1.3 76.4 - - - +
81J PRO* 1.4 81.5 - - + +
82J ALA* 4.2 0.5 - - - +
99J CYS* 3.3 4.0 - - - +
100J GLU* 3.1 30.7 + - + +
102J PHE* 3.5 35.9 - - + -
106J ARG* 5.7 4.3 - - - +
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Residues in contact with PRO 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J TYR* 4.3 7.4 - - + -
54J VAL* 3.7 28.6 - - + +
57J LEU* 3.7 21.5 - - + +
58J PRO 3.7 22.9 - - - +
59J GLU* 4.3 5.4 - - + +
79J LEU 3.7 9.0 - - - +
80J VAL* 1.4 97.1 - - + +
82J ALA* 1.3 59.7 + - - +
97J VAL* 3.7 15.5 - - + -
98J LEU 3.8 6.1 - - - +
99J CYS* 4.1 1.8 - - - -
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Residues in contact with ALA 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54J VAL* 3.7 14.9 - - - +
80J VAL 4.2 4.9 - - - +
81J PRO* 1.3 74.9 - - - +
83J ALA* 1.3 60.6 + - + +
98J LEU* 2.8 21.0 + - + +
99J CYS 4.7 0.4 - - - -
100J GLU* 4.5 7.9 - - + +
114J ARG* 3.7 45.6 + - - +
216J ASP* 4.6 0.6 - - - +
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Residues in contact with ALA 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54J VAL* 4.0 5.8 - - - -
82J ALA* 1.3 82.0 - - - +
84J MET* 1.3 61.7 + - - +
85J PHE* 3.8 23.9 - - + -
96J LEU 3.8 0.5 - - - +
97J VAL* 3.4 2.4 - - - -
98J LEU* 2.8 37.4 + - + +
216J ASP* 3.9 26.7 - - + +
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Residues in contact with MET 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J PRO* 3.8 24.7 - - - +
52J LYS 4.0 3.8 - - - +
53J CYS* 3.7 36.1 - - - +
54J VAL* 4.0 20.1 - - + +
57J LEU* 3.9 21.5 - - + -
83J ALA* 1.3 72.2 - - - +
85J PHE* 1.3 82.5 + - - +
95J LYS* 4.1 26.5 - - + +
96J LEU 3.3 8.7 - - - +
97J VAL* 4.5 1.1 - - - +
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Residues in contact with PHE 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83J ALA* 3.8 26.7 - - + -
84J MET* 1.3 82.2 - - - +
86J ARG* 1.3 67.7 + - - +
95J LYS* 3.4 12.7 - - - +
96J LEU* 2.7 38.9 + - + +
186J ALA* 3.5 17.9 - - + +
187J GLY* 3.5 28.3 - - - -
188J VAL* 3.8 13.5 - - + -
216J ASP 4.5 0.9 - - - -
217J HIS* 3.7 32.8 - + - -
220J VAL* 3.5 38.1 - - + -
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Residues in contact with ARG 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I PRO* 5.2 4.9 + - - +
22I GLN 5.9 1.0 + - - -
85J PHE* 1.3 75.6 - - - +
87J ASP* 1.3 60.2 + - - +
88J PRO* 3.2 6.5 - - - +
92J ASP* 2.4 47.3 + - - +
94J ASN 4.0 4.7 - - - -
95J LYS* 4.6 11.9 - - - +
96J LEU* 4.2 2.3 - - - +
184J LEU 5.1 1.0 + - - -
185J TYR* 3.1 66.1 + - + +
186J ALA* 2.9 32.8 + - - +
187J GLY* 5.8 0.7 - - - -
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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