Contacts of the strand formed by residues 95 - 102 (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 LYS 95 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26J VAL* 4.8 1.1 - - + -
27J GLN 2.9 12.0 + - - +
28J ALA* 3.6 5.7 - - + -
29J MET* 2.9 25.1 + - - +
50J GLU* 3.1 24.0 + - - -
51J PRO* 3.7 40.5 + - + -
57J LEU* 5.5 0.2 - - + -
84J MET* 4.1 25.8 - - + +
85J PHE 3.4 15.3 - - - +
86J ARG* 4.6 9.3 - - - +
87J ASP* 3.8 15.5 - - - +
92J ASP* 4.6 8.3 + - - -
93J PRO 3.4 17.4 + - - +
94J ASN* 1.3 83.5 + - - +
96J LEU* 1.3 60.2 + - - +
97J VAL* 4.5 7.2 - - + -
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Residues in contact with LEU 96 (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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29J MET* 3.5 20.2 - - + -
31J ILE* 3.9 22.2 - - + -
83J ALA 3.8 0.3 - - - +
84J MET* 3.3 3.3 - - - +
85J PHE* 2.7 47.6 + - + +
86J ARG 4.2 3.1 - - - +
87J ASP* 3.6 32.5 - - - +
88J PRO* 4.0 17.9 - - + -
89J PHE* 4.6 4.7 - - + -
95J LYS* 1.3 73.0 - - - +
97J VAL* 1.3 63.2 + - - +
98J LEU 4.2 0.7 - - - -
220J VAL* 4.0 23.3 - - + -
223J PHE* 4.3 7.6 - - + -
224J ILE* 4.1 15.7 - - + -
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Residues in contact with VAL 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J ALA* 4.5 3.4 - - + -
29J MET 2.9 13.3 + - - +
30J TYR* 3.3 20.6 - - + -
31J ILE* 2.6 36.7 + - - +
54J VAL* 4.7 0.4 - - + -
57J LEU* 3.2 40.2 - - + -
81J PRO* 3.7 21.8 - - + -
83J ALA 3.4 10.3 - - - +
84J MET* 4.7 0.2 - - + -
95J LYS* 4.5 9.4 - - + -
96J LEU* 1.3 80.4 - - - +
98J LEU* 1.3 66.8 + - - +
99J CYS* 3.6 4.0 + - - -
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Residues in contact with LEU 98 (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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31J ILE* 3.6 33.7 - - + +
32J TRP* 4.9 2.7 - - - +
33J ILE* 5.3 6.5 - - + -
40J LEU* 5.0 3.1 - - + -
81J PRO 3.7 0.7 - - - -
82J ALA* 2.8 27.9 + - + +
83J ALA* 2.8 20.0 + - + +
96J LEU 4.2 0.2 - - - -
97J VAL* 1.3 75.9 - - - +
99J CYS* 1.3 66.1 + - - +
114J ARG* 5.3 3.6 - - - +
216J ASP* 3.7 47.1 - - + +
219J TRP* 4.1 22.4 - - + -
220J VAL* 4.0 15.1 - - + +
349J PHE* 4.7 7.6 - - + -
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Residues in contact with CYS 99 (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* 3.5 35.2 - - - -
31J ILE 2.8 18.6 + - - +
32J TRP* 4.1 10.3 - - - +
33J ILE* 4.9 3.8 + - - +
79J LEU* 3.7 23.1 - - + -
80J VAL 3.3 10.5 - - - +
81J PRO* 4.1 15.3 - - - -
82J ALA* 4.3 3.1 - - - +
97J VAL* 3.7 11.2 - - - -
98J LEU* 1.3 87.6 - - - +
100J GLU* 1.3 62.0 + - - +
101J VAL* 4.2 0.5 + - - +
114J ARG* 5.9 0.9 - - - -
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Residues in contact with GLU 100 (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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78J TYR 3.7 0.2 - - - +
79J LEU* 3.6 5.2 - - - -
80J VAL* 3.1 33.7 + - + +
82J ALA* 4.5 5.0 - - + +
99J CYS* 1.3 73.6 - - - +
101J VAL* 1.3 63.2 + - - +
102J PHE* 3.3 19.2 - - + -
112J ASN* 3.0 32.7 + - - +
114J ARG* 3.0 50.4 + - + +
115J HIS* 3.2 26.1 + - - -
118J LYS* 5.6 1.2 - - - +
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Residues in contact with VAL 101 (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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32J TRP* 3.8 29.2 - - + -
33J ILE 3.6 24.9 - - - +
62J PHE* 3.9 18.6 - - + -
69J GLN* 4.1 4.3 - - - +
77J MET* 3.7 18.8 - - + -
78J TYR 3.4 3.8 - - - -
79J LEU* 4.6 0.9 - - + -
99J CYS 5.0 0.4 - - - +
100J GLU* 1.3 73.3 - - - +
102J PHE* 1.3 64.9 + - - +
109J ALA* 3.1 40.3 + - + +
111J THR 6.3 0.2 - - - -
112J ASN* 3.1 19.3 + - + +
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Residues in contact with PHE 102 (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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77J MET* 3.5 13.4 - - - +
78J TYR* 3.1 44.0 + - + -
80J VAL* 3.5 35.7 - - + -
100J GLU* 3.3 39.9 - - + -
101J VAL* 1.3 75.2 - - - +
103J LYS* 1.3 62.0 + - - +
106J ARG* 3.5 28.5 - - - +
107J ARG 3.4 5.8 - - - +
108J PRO* 3.6 22.4 - - + -
109J ALA 4.1 0.7 - - - +
112J ASN* 3.9 1.8 - - - -
115J HIS* 3.9 25.1 - + - -
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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