Contacts of the strand formed by residues 95 - 102 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C VAL* 4.8 0.9 - - + -
27C GLN 3.0 11.6 + - - +
28C ALA* 3.6 7.1 - - + -
29C MET* 2.9 28.6 + - - +
50C GLU* 2.6 29.4 + - - -
51C PRO* 3.5 37.7 - - + -
57C LEU* 5.5 0.2 - - + -
84C MET* 3.9 28.3 - - + -
85C PHE 3.3 14.6 - - - +
86C ARG* 4.8 7.7 - - - +
87C ASP* 3.9 9.3 - - - +
92C ASP* 4.5 7.7 + - - -
93C PRO* 3.5 18.7 + - - +
94C ASN* 1.3 81.7 + - - +
96C LEU* 1.3 66.1 + - - +
97C VAL* 4.6 4.9 - - + -
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C MET* 3.6 24.7 - - + -
31C ILE* 4.0 9.6 - - + -
83C ALA 4.0 0.2 - - - +
84C MET* 3.4 3.5 - - - +
85C PHE* 2.8 42.3 + - + +
86C ARG 4.0 4.3 - - - +
87C ASP* 3.4 34.7 - - - +
88C PRO* 3.8 20.4 - - + -
89C PHE* 4.6 5.8 - - + -
95C LYS* 1.3 74.8 - - - +
97C VAL* 1.3 62.7 + - - +
98C LEU 4.2 0.4 - - - -
220C VAL* 4.1 11.9 - - + -
223C PHE* 4.4 14.1 - - + -
224C ILE* 3.9 26.9 - - + -
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ALA* 4.6 2.7 - - + -
29C MET 2.8 14.8 + - - +
30C TYR* 3.5 16.4 - - + -
31C ILE* 2.9 29.6 + - - +
54C VAL* 4.6 0.9 - - + -
57C LEU* 3.2 36.6 - - + -
81C PRO* 3.6 32.5 - - + -
82C ALA 4.5 0.4 - - - +
83C ALA 3.4 7.9 - - - +
84C MET* 4.7 0.4 - - + -
95C LYS* 4.6 8.5 - - + -
96C LEU* 1.3 80.4 - - - +
98C LEU* 1.3 68.8 + - - +
99C CYS* 3.7 8.9 + - - -
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Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ILE* 3.6 32.7 - - + +
32C TRP* 4.9 1.8 - - - -
33C ILE* 5.5 5.8 - - + -
40C LEU* 4.9 4.9 - - + -
82C ALA* 2.8 25.8 + - + +
83C ALA* 2.8 19.8 + - + +
96C LEU 4.2 0.6 - - - -
97C VAL* 1.3 75.3 - - - +
99C CYS* 1.3 66.4 + - - +
114C ARG* 5.2 3.4 - - - +
216C ASP* 3.8 45.8 - - + +
219C TRP* 4.2 22.9 - - + -
220C VAL* 3.9 18.9 - - + +
349C PHE* 4.6 8.7 - - + -
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Residues in contact with CYS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C TYR* 3.5 36.6 - - - -
31C ILE 2.9 17.9 + - - +
32C TRP* 4.4 7.6 - - - +
33C ILE* 5.2 4.3 + - - +
79C LEU* 4.1 17.7 - - + -
80C VAL 3.3 11.7 - - - +
81C PRO* 3.9 9.9 - - - -
82C ALA* 4.1 2.9 - - - +
97C VAL* 3.8 18.4 - - - -
98C LEU* 1.3 86.3 - - - +
100C GLU* 1.3 68.7 + - - +
101C VAL* 4.2 1.0 + - - +
114C ARG* 5.7 1.1 - - - -
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Residues in contact with GLU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C TYR 3.5 0.5 - - - +
79C LEU* 3.5 4.7 - - - -
80C VAL* 2.8 37.2 + - + +
82C ALA* 4.4 3.7 - - + +
99C CYS* 1.3 72.2 - - - +
101C VAL* 1.3 62.8 + - - +
102C PHE* 3.5 17.6 - - + -
112C ASN* 3.1 23.8 + - - +
114C ARG* 3.0 54.7 + - + +
115C HIS* 3.2 33.0 + - - +
118C LYS* 5.3 2.3 - - - +
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Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C TRP* 3.7 40.4 - - + -
33C ILE* 3.9 12.1 - - + +
62C PHE* 3.9 19.5 - - + -
69C GLN* 4.2 4.0 - - - +
77C MET* 4.0 12.8 - - + -
78C TYR 3.2 9.4 - - - +
79C LEU* 4.3 4.3 - - + -
99C CYS 5.0 0.9 - - - +
100C GLU* 1.3 70.9 - - - +
102C PHE* 1.3 67.1 + - - +
109C ALA* 3.2 31.4 + - + -
111C THR 6.3 0.2 - - - -
112C ASN* 3.0 25.4 + - + +
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Residues in contact with PHE 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C MET* 3.5 12.5 - - - +
78C TYR* 3.0 41.6 + - + -
80C VAL* 3.6 31.0 - - + -
100C GLU* 3.5 44.6 - - + -
101C VAL* 1.3 74.2 - - - +
103C LYS* 1.3 64.2 + - - +
106C ARG* 3.5 30.3 - - - +
107C ARG 3.3 6.7 - - - +
108C PRO* 3.7 21.8 - - + -
109C ALA 3.9 1.3 - - - +
112C ASN* 4.1 1.3 - - - -
115C HIS* 4.1 23.1 - + - -
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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