Contacts of the strand formed by residues 111 - 119 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU* 5.7 2.2 - - + -
36B PHE* 3.6 35.0 - + - -
39B LEU* 3.7 36.3 - - + -
49B ILE* 5.1 1.6 - - + -
76B PRO 4.9 1.6 - - - -
77B ASP* 4.1 35.9 - - + -
78B ASP 3.5 4.3 + - - -
79B ILE* 3.2 20.8 - - + -
80B TYR* 2.4 38.2 + - - +
101B ILE* 4.3 18.2 - - + -
102B ARG 3.2 25.8 - - - +
103B PRO* 3.6 22.2 - - + -
104B PRO* 4.5 0.4 - - - -
110B TYR* 1.3 75.9 - - - +
112B ALA* 1.3 58.2 + - - +
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ILE* 4.3 2.7 - - - -
80B TYR* 3.8 14.4 - - + -
101B ILE* 3.3 8.8 - - - +
102B ARG* 3.2 68.2 + - - +
108B GLU* 5.2 1.1 - - - +
110B TYR 3.7 2.8 + - - +
111B PHE* 1.3 73.7 - - - +
113B LEU* 1.3 63.6 + - - +
114B LEU* 3.8 2.9 - - + +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LEU* 5.4 3.8 - - + -
79B ILE* 4.2 8.3 - - + -
80B TYR 3.5 14.6 + - - +
81B VAL* 4.8 17.3 - - + -
82B SER 5.9 0.2 - - - +
85B GLN* 2.5 49.8 + - + +
91B LEU* 5.8 3.4 - - + -
97B ILE* 3.7 27.1 - - + -
99B GLY* 4.1 15.9 - - - +
100B LYS 3.4 18.4 - - - +
101B ILE* 4.3 6.5 - - + -
112B ALA* 1.3 74.1 - - - +
114B LEU* 1.3 59.0 + - - +
115B LYS 4.0 17.3 - - - +
116B VAL* 4.6 8.7 - - + +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B GLN* 3.6 14.4 + - - +
100B LYS* 3.3 30.9 + - + +
101B ILE 3.9 3.4 - - - +
102B ARG* 3.7 55.6 - - + +
112B ALA* 3.8 5.8 - - + +
113B LEU* 1.3 78.2 - - - +
115B LYS* 1.3 64.3 + - + +
486I THR* 5.1 7.8 - - - +
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Residues in contact with LYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLY* 3.3 2.9 - - - -
100B LYS* 3.2 32.5 + - + +
113B LEU* 4.0 3.9 - - - +
114B LEU* 1.3 81.5 - - + +
116B VAL* 1.3 71.1 + - - +
117B ASN* 3.7 15.9 - - - +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B GLN* 6.4 0.2 - - - -
89B PHE* 3.9 41.7 - - + -
91B LEU* 6.2 3.4 - - + -
97B ILE* 3.8 30.3 - - + -
98B SER 4.2 0.4 - - - +
99B GLY* 4.2 4.5 - - - -
113B LEU* 4.6 9.2 - - + +
115B LYS* 1.3 83.6 - - + +
117B ASN* 1.3 66.5 + - - +
118B GLU 3.9 7.4 - - - +
119B VAL* 3.7 29.8 - - + -
124B PRO* 4.9 7.3 - - + +
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Residues in contact with ASN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PHE* 3.6 27.3 - - - -
98B SER* 2.9 11.5 + - - +
99B GLY* 3.6 18.9 - - - -
100B LYS* 3.8 2.5 + - - +
115B LYS* 3.7 21.4 + - - +
116B VAL* 1.3 80.2 - - - +
118B GLU* 1.3 62.7 + - + +
123B LYS* 5.4 0.5 - - - -
124B PRO* 4.0 16.7 - - - +
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B THR* 3.5 4.0 - - - +
97B ILE* 3.8 1.4 - - - -
98B SER* 3.0 43.6 + - - +
116B VAL* 3.8 1.4 - - - +
117B ASN* 1.3 79.9 - - + +
119B VAL* 1.3 63.9 + - - +
121B PHE* 3.2 37.1 - - - +
122B ASP* 3.3 25.4 - - - +
123B LYS* 5.5 0.4 - - - +
124B PRO* 4.9 0.2 - - - -
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B PHE* 6.0 3.4 - - + -
91B LEU* 4.5 13.9 - - + -
95B ASP* 4.8 0.7 - - + -
96B THR 3.4 2.5 - - - -
97B ILE* 4.1 15.3 - - + -
116B VAL* 3.7 22.7 - - + -
118B GLU* 1.3 74.2 - - - +
120B ASN* 1.3 89.2 + - - +
121B PHE 3.2 0.4 - - - -
122B ASP* 2.9 29.0 + - - +
123B LYS 4.6 0.7 - - - +
124B PRO* 3.9 25.1 - - + -
127B ALA* 3.9 23.2 - - + +
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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