Contacts of the strand formed by residues 94 - 103 (chain F) in PDB entry 3FFC
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 THR 94 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F THR* 4.2 8.1 - - + -
11F ALA 3.4 5.8 - - - +
12F MET* 3.7 15.2 - - + +
78F LEU* 4.7 0.2 - - - -
92F SER* 5.3 0.3 + - - -
93F HIS* 1.3 75.8 - - - +
95F LEU* 1.3 63.6 + - - +
96F GLN* 3.7 27.8 - - + +
117F ALA 3.9 0.2 - - - +
118F TYR* 3.4 9.3 - - - -
119F ASP* 2.8 36.6 + - - -
31G HIS* 4.2 19.4 - - - -
32G PRO* 4.6 9.9 - - - +
33G SER* 5.0 1.0 + - - -
62G PHE* 3.8 20.1 - - + -
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Residues in contact with LEU 95 (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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10F THR* 3.4 2.8 - - - -
11F ALA* 2.8 39.3 + - + +
74F ASP* 4.0 29.2 - - + +
77F SER* 3.6 29.6 - - - +
78F LEU* 4.1 13.2 - - + +
81F LEU* 3.9 11.7 - - + -
94F THR* 1.3 75.0 - - - +
96F GLN* 1.3 69.8 + - - +
97F SER* 5.9 1.1 - - - -
116F TYR* 4.0 16.6 - - + -
117F ALA 3.6 11.2 - - - +
118F TYR* 4.6 1.3 - - + -
9H LEU* 3.8 29.6 - - + -
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Residues in contact with GLN 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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9F ASP 3.2 6.5 - - - +
10F THR* 3.7 12.8 - - - +
94F THR* 3.7 8.6 - - + +
95F LEU* 1.3 81.6 - - - +
97F SER* 1.3 61.0 + - - +
116F TYR* 3.3 9.8 - - - -
117F ALA* 2.8 37.2 + - - +
120F GLY* 4.3 5.5 + - - -
31G HIS* 3.0 24.9 + - - -
56G PHE* 3.1 32.2 - - + -
60G TRP* 3.0 44.9 + - + +
62G PHE* 3.5 13.4 - - - -
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Residues in contact with SER 97 (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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7F TYR 4.5 0.4 - - - -
8F PHE* 3.6 0.3 - - - -
9F ASP* 2.8 46.6 + - - +
95F LEU* 5.9 1.1 - - - -
96F GLN* 1.3 75.2 - - - +
98F MET* 1.3 62.6 + - - +
99F TYR* 3.8 16.3 - - - -
114F ASN* 3.9 4.0 + - - -
115F GLN 3.4 5.4 - - - -
116F TYR* 3.7 29.7 + - - -
56G PHE* 3.4 5.7 - - - -
60G TRP* 4.1 1.6 - - - -
3H ARG* 4.1 0.2 + - - -
5H ARG* 3.9 11.8 + - - -
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Residues in contact with MET 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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6F ARG* 4.3 10.8 - - + +
7F TYR 3.3 5.6 - - - +
8F PHE* 3.5 39.7 - - + -
97F SER* 1.3 74.0 + - - +
99F TYR* 1.3 61.7 + - - +
113F HIS* 4.3 2.2 - - + +
114F ASN* 3.3 2.4 + - - +
115F GLN* 3.0 65.8 + - + +
56G PHE* 4.3 4.7 - - - -
57G SER 4.1 3.6 - - - +
58G LYS* 3.6 40.2 - - + +
60G TRP* 3.7 17.0 - - + -
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Residues in contact with TYR 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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6F ARG* 3.2 9.3 - - - +
7F TYR* 2.6 70.6 + + + -
9F ASP* 3.3 23.6 + - - -
70F ASN* 5.0 0.2 + - - -
97F SER* 3.8 10.8 - - - -
98F MET* 1.3 77.1 - - - +
100F GLY* 1.3 60.1 + - - +
113F HIS 3.5 11.9 - - - +
114F ASN* 3.6 16.2 - - + +
159F TYR* 3.6 20.2 - + - -
160F LEU* 5.1 0.7 - - + -
2H LEU* 3.2 22.0 - - - +
3H ARG* 3.0 66.1 + - + +
5H ARG* 4.0 1.3 - - - -
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Residues in contact with GLY 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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5F MET* 3.1 12.8 - - - -
6F ARG* 3.5 7.1 + - - +
7F TYR* 5.7 0.2 - - - -
99F TYR* 1.3 83.6 - - - +
101F CYS* 1.3 58.9 + - - -
113F HIS* 2.8 36.3 + - - +
159F TYR* 4.8 0.7 - - - -
160F LEU* 3.4 12.2 - - - +
164F CYS* 4.0 8.3 - - - -
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Residues in contact with CYS 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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4F SER* 3.4 1.7 - - - -
5F MET* 2.9 31.6 + - - -
6F ARG* 3.7 4.5 - - - -
100F GLY* 1.3 73.9 - - - -
102F ASP* 1.3 60.7 + - - +
103F VAL* 3.9 2.0 + - - -
109F LEU* 3.4 23.8 - - + -
111F ARG 3.4 4.3 - - - -
160F LEU* 3.9 4.9 - - + +
164F CYS* 2.1 59.0 - - + -
165F VAL* 3.7 7.6 - - - -
168F LEU* 4.2 12.8 - - - +
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Residues in contact with ASP 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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3F HIS 3.5 7.0 - - - +
4F SER* 3.1 12.7 - - - -
6F ARG* 2.8 31.4 + - - -
101F CYS* 1.3 70.8 - - - +
103F VAL* 1.3 54.8 + - - +
109F LEU* 3.6 2.8 - - - -
110F LEU* 2.7 42.4 + - + +
111F ARG* 2.8 27.9 + - + +
113F HIS* 3.0 23.4 + - - -
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Residues in contact with VAL 103 (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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2F SER* 3.1 18.5 - - - -
3F HIS* 2.9 30.6 + - + +
101F CYS* 3.9 3.3 + - - -
102F ASP* 1.3 76.6 - - - +
104F GLY* 1.3 66.1 + - - +
107F GLY* 3.7 25.8 - - - +
108F ARG 3.2 12.3 - - - +
109F LEU* 4.3 0.4 - - - -
110F LEU* 3.7 6.7 - - - +
165F VAL* 3.9 26.0 - - + +
168F LEU* 3.4 34.8 - - + -
172F LEU* 4.6 6.5 - - + -
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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