Contacts of the strand formed by residues 95 - 102 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26F VAL* 4.8 0.7 - - + -
27F GLN 3.0 11.7 + - - +
28F ALA* 3.6 5.3 - - + -
29F MET* 2.9 30.5 + - - +
50F GLU* 2.8 27.0 + - - -
51F PRO* 3.4 42.3 + - + -
84F MET* 4.0 25.8 - - + +
85F PHE 3.4 14.4 - - - +
86F ARG* 4.7 8.5 - - - +
87F ASP* 3.8 4.8 - - - +
92F ASP* 4.3 10.9 + - - -
93F PRO 3.4 18.2 + - - +
94F ASN* 1.3 81.3 - - - +
96F LEU* 1.3 62.2 + - - +
97F VAL* 4.2 8.3 - - + -
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Residues in contact with LEU 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F MET* 3.6 24.9 - - + -
31F ILE* 4.0 14.4 - - + -
83F ALA 3.9 0.4 - - - +
84F MET* 3.3 4.3 - - - +
85F PHE* 2.7 43.5 + - + +
86F ARG 4.2 3.8 - - - +
87F ASP* 3.4 35.2 - - - +
88F PRO* 3.7 21.3 - - + -
89F PHE* 4.3 7.4 - - + -
95F LYS* 1.3 71.4 - - - +
97F VAL* 1.3 62.8 + - - +
98F LEU 4.2 0.7 - - - -
186F ALA* 5.1 0.9 - - + -
220F VAL* 4.3 11.0 - - + -
223F PHE* 4.3 9.2 - - + -
224F ILE* 4.0 25.8 - - + -
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Residues in contact with VAL 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F ALA* 4.6 9.9 - - + -
29F MET 2.9 15.0 + - - +
30F TYR* 3.3 12.5 - - + -
31F ILE* 2.7 33.7 + - - +
54F VAL* 4.8 0.2 - - + -
57F LEU* 3.4 35.9 - - + -
81F PRO* 3.9 21.1 - - + -
83F ALA 3.3 7.4 - - - +
84F MET* 4.3 0.4 - - + -
95F LYS* 4.2 13.5 - - + +
96F LEU* 1.3 81.9 - - - +
98F LEU* 1.3 66.9 + - - +
99F CYS* 3.5 6.4 - - - -
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Residues in contact with LEU 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F ILE* 3.8 29.4 - - + +
32F TRP* 5.1 2.9 - - - +
33F ILE* 5.4 5.4 - - + -
40F LEU* 5.2 2.9 - - + -
81F PRO* 3.8 1.4 - - - +
82F ALA* 2.8 31.9 + - + -
83F ALA* 2.7 25.3 + - + +
96F LEU 4.2 0.2 - - - -
97F VAL* 1.3 73.6 - - - +
99F CYS* 1.3 67.3 + - - +
114F ARG* 5.0 4.7 - - - +
216F ASP* 3.7 46.2 - - + +
219F TRP* 4.1 22.4 - - + -
220F VAL* 3.9 17.8 - - + +
349F PHE* 4.5 9.0 - - + -
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Residues in contact with CYS 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F TYR* 3.4 36.8 - - - -
31F ILE 2.9 19.0 + - - +
32F TRP* 4.4 7.6 - - - +
33F ILE* 5.1 5.2 + - - +
79F LEU* 4.0 19.3 - - + -
80F VAL 3.3 11.4 - - - +
81F PRO* 4.1 12.6 - - - -
82F ALA* 4.2 3.8 - - - +
97F VAL* 3.5 15.0 - - - -
98F LEU* 1.3 85.4 - - - +
100F GLU* 1.3 67.6 + - - +
101F VAL* 4.3 0.7 + - - +
114F ARG* 5.6 1.7 - - - -
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Residues in contact with GLU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F TYR 3.6 2.9 - - - +
79F LEU* 3.6 2.4 - - - -
80F VAL* 3.1 34.9 + - + +
82F ALA* 4.3 4.3 - - + +
99F CYS* 1.3 73.6 - - - +
101F VAL* 1.3 61.0 + - - +
102F PHE* 3.2 18.4 - - + -
112F ASN* 2.8 38.5 + - - +
114F ARG* 3.1 46.0 + - + +
115F HIS* 3.2 31.9 + - - -
118F LYS* 5.4 2.1 - - - +
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Residues in contact with VAL 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F TRP* 3.8 35.2 - - + -
33F ILE 3.9 17.3 - - - +
62F PHE* 3.8 16.2 - - + -
69F GLN* 4.4 3.8 - - - +
77F MET* 3.5 29.8 - - + -
78F TYR 3.3 9.4 - - - +
79F LEU* 4.3 1.3 - - + -
99F CYS 5.1 0.4 - - - +
100F GLU* 1.3 76.0 - - - +
102F PHE* 1.3 64.6 + - - +
109F ALA* 3.0 29.7 + - + +
111F THR* 5.8 1.1 - - - +
112F ASN* 3.1 19.9 + - + +
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Residues in contact with PHE 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F MET* 3.4 13.3 - - - +
78F TYR* 3.0 38.3 + - + -
80F VAL* 3.7 34.1 - - + -
100F GLU* 3.2 39.0 - - + -
101F VAL* 1.3 75.0 - - - +
103F LYS* 1.3 63.8 + - - +
106F ARG* 3.6 26.2 - - - +
107F ARG 3.4 5.4 - - - +
108F PRO* 3.5 26.5 - - + -
109F ALA 4.0 0.7 - - - +
112F ASN* 4.0 4.3 - - - -
115F HIS* 3.9 24.2 - + - -
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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