Contacts of the strand formed by residues 98 - 108 (chain A) in PDB entry 6TAV
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 GLU 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A SER* 3.7 12.9 + - - -
97A ASN* 1.3 82.9 - - + +
99A GLU* 1.3 59.9 + - - +
100A VAL* 5.6 1.4 - - - +
121A MET* 3.3 31.4 - - + +
122A VAL 3.6 7.4 - - - +
123A LYS* 4.2 15.4 + - + +
634A LEU* 3.2 40.5 - - + +
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Residues in contact with GLU 99 (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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66A SER* 3.2 23.9 + - - -
67A VAL* 4.8 4.6 + - + +
71A ARG* 3.3 13.9 + - - -
94A SER* 2.7 36.3 + - - +
96A SER* 4.1 9.5 + - - +
98A GLU* 1.3 73.5 - - - +
100A VAL* 1.3 70.7 + - - +
101A MET* 3.2 33.2 - - + +
121A MET* 3.7 1.7 - - - +
122A VAL* 3.0 35.0 + - + +
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Residues in contact with VAL 100 (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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67A VAL* 3.4 28.8 - - + +
98A GLU 5.6 1.1 - - - +
99A GLU* 1.3 81.7 - - - +
101A MET* 1.3 66.7 + - - +
119A THR* 4.0 26.2 - - + -
120A VAL 3.6 13.7 - - - +
121A MET* 4.3 17.5 - - + -
634A LEU* 3.9 22.2 - - + +
635A ASN* 5.2 4.5 - - + +
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Residues in contact with MET 101 (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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64A LEU* 3.7 31.4 - - + -
65A GLU* 3.7 11.0 - - - +
66A SER* 4.4 7.0 - - - +
67A VAL* 4.2 6.1 - - - -
71A ARG* 4.4 20.9 - - - +
91A VAL* 5.8 0.7 - - - -
92A PRO* 5.5 9.0 - - + +
93A LYS 5.6 0.2 - - - +
94A SER* 4.6 7.4 - - - -
99A GLU* 3.2 39.9 + - + +
100A VAL* 1.3 79.7 - - - +
102A PHE* 1.3 64.8 + - - +
103A LEU 3.8 0.3 + - - -
119A THR* 3.6 4.0 - - - -
120A VAL* 3.0 35.1 + - - +
122A VAL* 3.8 25.6 - - + -
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Residues in contact with PHE 102 (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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63A SER 3.7 1.7 - - - +
64A LEU* 3.5 3.0 - - - +
65A GLU* 2.8 52.3 + - + +
66A SER 4.0 6.7 - - - -
67A VAL* 3.7 44.2 - - + -
101A MET* 1.3 71.2 - - - +
103A LEU* 1.3 59.6 + - - +
104A THR* 4.9 2.9 - - + -
117A ARG* 3.8 34.5 - - + -
118A THR 3.9 1.8 - - - -
119A THR* 3.7 27.1 - - + -
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Residues in contact with LEU 103 (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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35A VAL* 4.2 31.4 - - + -
39A LEU* 5.0 7.0 - - + -
62A ALA* 4.3 11.7 - - + -
63A SER 3.6 30.3 - - - +
64A LEU* 3.7 15.5 - - + +
89A PHE* 6.4 0.4 - - + -
101A MET 3.8 1.0 + - - -
102A PHE* 1.3 72.3 - - - +
104A THR* 1.3 65.0 + - - +
105A VAL* 5.0 9.1 - - + +
116A LYS 4.1 0.3 - - - +
117A ARG* 3.6 0.5 - - - -
118A THR* 3.1 34.2 + - - +
120A VAL* 3.4 30.3 - - + -
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Residues in contact with THR 104 (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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61A SER 3.9 0.2 - - - +
63A SER* 3.0 34.6 + - - -
65A GLU* 3.7 19.6 + - - +
102A PHE* 4.9 2.9 - - + -
103A LEU* 1.3 77.8 - - - +
105A VAL* 1.3 64.6 + - - +
106A GLN* 5.3 0.9 - - - +
115A LYS* 5.4 12.8 + - - -
116A LYS 3.2 10.5 - - - -
117A ARG* 3.4 46.2 - - + +
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Residues in contact with VAL 105 (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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33A VAL* 4.0 31.9 - - + +
35A VAL* 5.8 1.6 - - + -
60A VAL* 3.9 26.0 - - + -
61A SER 3.7 7.9 - - - +
62A ALA* 4.1 15.5 - - + +
103A LEU* 5.0 10.3 - - + -
104A THR* 1.3 77.3 - - - +
106A GLN* 1.3 64.9 + - - +
107A VAL* 5.2 5.6 - - + -
115A LYS* 3.3 21.2 - - - +
116A LYS* 3.1 18.4 + - + +
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Residues in contact with GLN 106 (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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59A THR 3.6 1.9 - - - +
60A VAL* 3.6 1.6 - - - -
61A SER* 2.9 50.4 + - - +
63A SER* 5.3 4.8 + - - +
104A THR* 5.3 0.9 - - - +
105A VAL* 1.3 76.5 - - - +
107A VAL* 1.3 71.1 + - - +
108A LYS* 3.5 34.2 + - + +
113A GLU* 5.0 3.4 + - + +
114A PHE 3.7 9.9 - - - +
115A LYS* 4.3 28.8 + - + +
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Residues in contact with VAL 107 (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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31A TYR* 4.6 25.4 - - + -
33A VAL* 6.1 1.6 - - + -
51A LEU* 5.9 1.3 - - + -
58A VAL* 3.3 29.6 - - + -
59A THR 3.8 3.4 - - - +
60A VAL* 4.0 24.7 - - + +
105A VAL* 5.2 5.8 - - + -
106A GLN* 1.3 74.7 - - - +
108A LYS* 1.3 57.2 + - - +
109A GLY 3.9 0.2 + - - -
112A GLN 4.1 2.4 - - - +
113A GLU* 3.4 9.5 - - - +
114A PHE* 3.0 61.2 + - + +
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Residues in contact with LYS 108 (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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58A VAL* 3.1 15.8 - - - +
59A THR* 3.0 36.5 + - - +
61A SER* 5.7 2.0 - - - +
106A GLN* 3.5 31.5 + - + +
107A VAL* 1.3 71.2 - - - +
109A GLY* 1.3 58.9 + - - +
110A PRO* 5.0 0.2 - - - +
113A GLU* 2.9 35.4 + - + +
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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