Contacts of the strand formed by residues 96 - 102 (chain F) in PDB entry 6XAV
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 96 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52F ASP* 5.1 5.2 - - + +
53F GLY* 3.4 25.4 - - - +
54F VAL* 3.8 17.3 - - + +
94F GLY 3.1 7.8 + - - -
95F ASP* 1.3 67.7 - - - +
97F ILE* 1.3 62.6 + - - +
98F SER* 5.7 2.2 - - - -
118F GLU 3.8 1.6 - - - +
119F VAL* 3.6 4.0 - - - -
120F ASN* 2.5 48.6 + - - -
121F PHE* 4.3 25.9 - - + +
249F LYS* 4.3 12.1 - - - +
253F LEU* 6.1 1.2 - - - +
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Residues in contact with ILE 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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52F ASP* 3.3 14.0 - - - -
53F GLY 3.2 7.0 + - - -
55F LEU* 4.9 2.5 - - + -
65F LEU* 3.3 35.6 - - + +
81F VAL* 6.0 0.7 - - + -
91F LEU* 3.7 39.5 - - + -
95F ASP* 3.1 16.5 + - + +
96F THR* 1.3 78.6 - - - +
98F SER* 1.3 64.6 + - - +
113F LEU* 3.7 30.5 - - + -
116F VAL* 3.7 15.7 - - + -
118F GLU 4.0 0.9 - - - -
119F VAL* 3.8 24.9 - - + -
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Residues in contact with SER 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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51F GLY 3.2 13.9 - - - -
52F ASP* 3.7 13.5 - - - -
96F THR* 5.5 2.9 - - - -
97F ILE* 1.3 77.9 - - - +
99F GLY* 1.3 57.8 + - - +
116F VAL* 3.9 0.5 - - - +
117F ASN* 2.9 21.4 + - - +
118F GLU* 3.0 40.1 + - - +
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Residues in contact with GLY 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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50F PHE* 3.5 6.3 - - - +
51F GLY 3.2 27.6 + - - -
65F LEU* 6.1 0.6 - - - +
97F ILE 4.3 0.6 - - - -
98F SER* 1.3 74.3 - - - +
100F LYS* 1.3 65.9 + - - -
101F ILE* 3.3 4.9 + - - +
113F LEU* 4.0 12.0 - - - +
115F LYS 3.3 11.0 - - - -
116F VAL* 4.1 0.7 - - - -
117F ASN* 3.3 15.9 - - - -
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Residues in contact with LYS 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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48F ASP* 3.5 42.1 + - + +
49F ILE 3.4 13.0 - - - +
50F PHE* 3.8 17.7 - - + -
99F GLY* 1.3 70.6 - - - -
101F ILE* 1.3 65.4 + - - +
113F LEU* 3.6 3.8 - - - +
114F LEU* 3.2 41.7 + - + +
115F LYS* 3.0 19.5 + - + +
117F ASN* 3.4 6.0 + - - +
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Residues in contact with ILE 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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3F LEU* 4.9 9.4 - - + -
39F LEU* 5.7 1.1 - - + -
49F ILE* 2.7 54.6 + - + +
50F PHE 3.8 7.4 - - - +
51F GLY* 3.7 21.3 - - - +
79F ILE* 3.7 44.0 - - + -
99F GLY 3.6 9.6 - - - +
100F LYS* 1.3 81.4 - - - +
102F ARG* 1.3 62.1 + - - +
111F PHE* 4.3 22.9 - - + -
112F ALA 3.3 10.8 - - - +
113F LEU* 4.2 7.4 - - + -
114F LEU* 4.0 2.9 - - - -
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Residues in contact with ARG 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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101F ILE* 1.3 75.9 - - - +
103F PRO* 1.3 84.1 + - + +
104F PRO* 4.7 0.2 - - - +
105F LYS* 3.4 46.9 - - - +
108F GLU* 4.1 19.6 + - - -
111F PHE* 3.2 25.3 - - - -
112F ALA* 3.2 30.9 + - + +
114F LEU* 3.7 32.5 - - + +
185G SER* 5.3 11.7 - - - -
187G ARG* 5.8 2.6 - - - +
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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