Contacts of the strand formed by residues 111 - 119 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ILE* 6.1 4.9 - - + -
77A ASP* 3.6 48.7 - - + -
78A ASP 3.3 4.5 + - - -
79A ILE* 3.2 21.7 - - + +
80A TYR* 2.4 33.5 + - - +
101A ILE* 4.3 19.3 - - + -
102A ARG 3.2 26.5 - - - +
103A PRO* 3.6 20.9 - - + -
104A PRO* 4.0 10.5 - - + -
110A TYR* 1.3 74.7 - - - +
112A ALA* 1.3 60.5 + - - +
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ILE* 4.7 0.2 - - - -
80A TYR* 3.8 15.9 - - + -
101A ILE* 3.5 4.7 - - - -
102A ARG* 3.1 70.4 + - - +
103A PRO 5.3 0.2 - - - -
108A GLU* 4.7 5.1 + - - +
110A TYR 3.5 3.6 + - - +
111A PHE* 1.3 72.7 - - - +
113A LEU* 1.3 63.9 + - - +
114A LEU* 3.6 2.4 + - + -
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 4.6 3.8 - - + -
79A ILE* 4.2 6.3 - - + -
80A TYR* 3.2 19.7 + - - +
81A VAL* 4.4 19.5 - - + +
82A SER* 4.8 3.6 + - - +
85A GLN* 2.4 49.6 + - + +
91A LEU* 5.9 3.1 - - + -
97A ILE* 3.7 27.8 - - + -
99A GLY* 4.2 12.6 - - - +
100A LYS 3.3 19.7 - - - +
101A ILE* 3.8 14.6 - - + -
112A ALA* 1.3 71.0 - - - +
114A LEU* 1.3 56.9 + - - +
115A LYS 4.1 13.9 - - - +
116A VAL* 4.6 7.4 - - + -
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A GLN* 3.0 16.7 + - - +
100A LYS* 3.1 34.0 + - + +
101A ILE 4.9 0.4 - - - -
102A ARG* 3.7 51.4 - - + +
112A ALA* 3.6 1.8 + - + +
113A LEU* 1.3 74.8 - - - +
115A LYS* 1.3 64.7 + - + +
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Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLN* 4.9 1.1 - - - +
89A PHE* 6.5 0.4 - - + -
99A GLY* 3.3 1.2 - - - -
100A LYS* 2.7 44.9 + - + +
113A LEU* 4.1 3.8 - - - +
114A LEU* 1.3 83.2 - - + +
116A VAL* 1.3 70.1 + - + +
117A ASN* 3.8 14.2 + - - +
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLN* 5.7 3.9 + - + +
89A PHE* 3.7 43.8 - - + -
91A LEU* 5.9 3.4 - - + -
97A ILE* 3.7 26.7 - - + -
98A SER 3.7 9.4 - - - +
99A GLY* 3.9 5.2 - - - -
113A LEU* 4.6 8.8 - - + +
115A LYS* 1.3 83.9 - - + +
117A ASN* 1.3 64.4 + - - +
118A GLU 3.8 4.7 - - - +
119A VAL* 3.7 28.0 - - + -
124A PRO* 4.9 6.4 - - + +
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Residues in contact with ASN 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PHE* 3.5 32.5 - - - -
98A SER 2.7 13.4 + - - +
99A GLY* 3.5 17.1 - - - -
100A LYS* 3.8 6.4 + - - +
115A LYS* 3.9 19.6 - - - +
116A VAL* 1.3 79.6 - - - +
118A GLU* 1.3 60.0 + - + +
123A LYS* 5.3 0.9 - - - -
124A PRO* 4.1 16.2 - - - +
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A THR* 3.6 2.4 - - - +
98A SER* 2.8 45.8 + - - +
116A VAL* 3.8 2.8 - - - +
117A ASN* 1.3 77.6 - - + +
119A VAL* 1.3 62.1 + - - +
121A PHE* 3.2 35.9 - - - +
122A ASP* 3.4 26.1 + - - +
124A PRO* 5.0 0.4 - - - -
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE* 5.4 3.4 - - + -
91A LEU* 4.3 15.9 - - + -
95A ASP* 4.8 1.8 - - + -
96A THR 3.4 2.7 - - - +
97A ILE* 4.0 19.3 - - + -
116A VAL* 3.7 23.1 - - + -
118A GLU* 1.3 75.1 - - - +
120A ASN* 1.3 86.6 + - - +
121A PHE 3.3 0.2 - - - -
122A ASP* 2.8 31.5 + - - +
123A LYS 4.7 1.0 - - - +
124A PRO* 4.0 23.3 - - + +
127A ALA* 4.3 21.1 - - + +
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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