Contacts of the strand formed by residues 111 - 119 (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 PHE 111 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3F LEU* 5.0 3.4 - - + -
36F PHE* 4.2 20.4 - + - -
39F LEU* 3.6 33.4 - - + -
49F ILE* 5.5 1.1 - - + -
76F PRO 4.8 1.1 - - - -
77F ASP* 3.6 49.1 - - + -
78F ASP 3.0 11.4 + - - +
79F ILE* 3.2 9.4 - - + -
80F TYR* 2.4 35.1 + - - +
101F ILE* 4.3 27.6 - - + -
102F ARG 3.2 26.2 - - - +
103F PRO* 3.6 22.4 - - + -
104F PRO* 4.1 3.6 - - + -
110F TYR* 1.3 72.4 - - - +
112F ALA* 1.3 58.9 + - - +
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Residues in contact with ALA 112 (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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79F ILE* 4.7 0.2 - - - -
80F TYR* 4.0 14.6 - - + -
101F ILE* 3.3 8.0 - - - -
102F ARG* 3.2 69.0 + - - +
103F PRO 5.4 0.2 - - - -
104F PRO* 5.7 0.2 - - - +
108F GLU* 5.1 3.4 - - - +
110F TYR 3.6 3.8 + - - +
111F PHE* 1.3 73.2 - - - +
113F LEU* 1.3 61.9 + - - +
114F LEU* 3.7 4.3 - - + +
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Residues in contact with LEU 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F LEU* 5.2 2.9 - - + -
79F ILE* 4.3 7.6 - - + -
80F TYR* 3.6 15.9 + - - +
81F VAL* 4.8 11.7 - - + -
85F GLN* 2.5 51.8 + - + +
91F LEU* 5.9 2.7 - - + -
97F ILE* 3.7 27.1 - - + -
99F GLY* 4.0 17.7 - - - +
100F LYS 3.6 16.8 - - - +
101F ILE* 4.2 8.3 - - + -
112F ALA* 1.3 72.5 - - - +
114F LEU* 1.3 60.5 + - - +
115F LYS 3.8 18.8 - - - +
116F VAL* 4.6 9.0 - - + +
184G TYR* 4.1 1.9 + - - -
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Residues in contact with LEU 114 (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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85F GLN* 4.1 4.4 + - - -
100F LYS* 3.2 33.1 + - + +
101F ILE 4.0 2.0 - - - -
102F ARG* 3.7 52.0 - - + +
112F ALA* 3.7 6.5 - - + +
113F LEU* 1.3 77.5 - - - +
115F LYS* 1.3 65.1 + - + +
184G TYR* 3.1 34.9 + - + +
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Residues in contact with LYS 115 (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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89F PHE* 6.5 0.2 - - - -
99F GLY* 3.3 1.7 - - - -
100F LYS* 3.0 35.2 + - + +
113F LEU* 3.8 4.6 - - - +
114F LEU* 1.3 82.1 - - + +
116F VAL* 1.3 73.7 + - + +
117F ASN* 3.8 17.9 + - - +
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Residues in contact with VAL 116 (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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89F PHE* 3.8 42.8 - - + -
97F ILE* 3.7 28.0 - - + -
98F SER 3.9 0.9 - - - +
99F GLY* 4.1 4.7 - - - -
113F LEU* 4.5 9.0 - - + +
115F LYS* 1.3 85.0 - - + +
117F ASN* 1.3 64.7 + - - +
118F GLU 3.8 9.0 - - - +
119F VAL* 3.7 30.1 - - + -
124F PRO* 4.6 9.7 - - + +
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Residues in contact with ASN 117 (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 19.4 - - - -
98F SER* 2.9 10.5 + - - +
99F GLY* 3.3 18.0 - - - -
100F LYS* 3.4 9.3 + - - +
115F LYS* 4.2 21.1 + - - +
116F VAL* 1.3 80.0 + - - +
118F GLU* 1.3 64.1 + - + +
123F LYS* 5.5 0.2 - - - -
124F PRO* 4.1 14.2 - - - +
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Residues in contact with GLU 118 (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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96F THR 3.8 2.3 - - - +
98F SER* 3.0 45.0 + - - +
116F VAL* 3.8 4.3 - - - +
117F ASN* 1.3 80.7 - - + +
119F VAL* 1.3 63.0 + - - +
121F PHE* 3.2 36.4 - - - +
122F ASP* 3.3 26.5 + - - +
124F PRO* 4.7 1.8 - - - -
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Residues in contact with VAL 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F PHE* 5.9 3.8 - - + -
91F LEU* 4.9 7.4 - - + -
95F ASP* 4.9 5.6 - - + +
96F THR 3.6 2.5 - - - -
97F ILE* 3.8 21.5 - - + -
116F VAL* 3.7 22.0 - - + -
118F GLU* 1.3 74.6 - - - +
120F ASN* 1.3 86.2 + - - +
121F PHE 3.2 0.7 - - - -
122F ASP* 2.9 27.5 + - - +
123F LYS 4.6 0.5 - - - +
124F PRO* 4.0 22.0 - - + +
127F ALA* 3.7 24.7 - - + -
256F HIS* 4.6 2.8 - - - -
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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