Contacts of the strand formed by residues 99 - 104 (chain A) in PDB entry 6XXD
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 VAL 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASP* 4.7 0.3 - - - +
93A GLY* 4.7 2.6 - - - -
94A HIS 5.3 0.3 + - - -
98A THR* 1.3 98.8 + - - +
100A TRP* 1.3 61.2 + - - +
101A PHE* 3.2 23.2 - - + -
111A LYS* 4.0 30.7 - - + +
112A THR 3.4 19.7 - - - +
113A ASN* 4.2 6.5 - - - +
114A THR 3.3 21.5 - - - +
115A ALA* 4.2 3.4 - - + -
116A VAL* 3.6 15.7 - - - +
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Residues in contact with TRP 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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77A THR* 3.2 37.7 - - + -
91A ILE* 3.6 20.2 - - + -
92A ALA 3.8 2.9 - - - -
93A GLY* 3.6 26.0 - - - -
99A VAL* 1.3 76.8 - - - +
101A PHE* 1.3 59.9 + - - +
111A LYS* 3.7 2.3 - - - -
112A THR* 3.0 41.8 + - + +
114A THR* 3.2 13.8 + - + -
115A ALA 2.9 30.6 + - - -
116A VAL* 3.7 14.3 - - + +
118A SER 3.5 12.2 + - - -
119A SER 3.6 3.4 + - - -
120A GLN* 3.7 41.1 - - + -
121A PRO* 3.6 19.1 - - + -
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Residues in contact with PHE 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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33A ASP* 3.8 42.2 - - + -
36A VAL* 3.6 17.3 - - + -
37A THR* 3.3 24.2 - - + -
40A LEU* 3.3 24.1 - - + +
91A ILE* 3.5 3.6 - - - -
92A ALA 2.8 37.0 + - - +
98A THR* 4.5 2.9 - - - -
99A VAL* 3.2 23.3 - - + -
100A TRP* 1.3 72.7 - - - +
102A ALA* 1.3 60.0 + - - +
109A VAL* 4.8 5.6 - - + -
110A TYR* 3.4 13.0 - - - +
111A LYS* 3.7 31.2 - - + -
112A THR* 5.5 0.2 - - - -
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Residues in contact with ALA 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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40A LEU* 3.9 0.3 - - - +
90A MET 3.4 6.7 - - - -
91A ILE* 3.8 10.7 - - + +
100A TRP 4.2 1.0 + - - -
101A PHE* 1.3 74.2 - - - +
103A ALA* 1.3 65.6 + - - +
108A GLY 4.6 0.9 - - - -
109A VAL* 3.6 6.8 - - - +
110A TYR* 2.8 57.9 + - + +
111A LYS* 4.7 0.4 - - - +
112A THR* 5.0 4.7 - - - +
124A CYS* 3.7 21.3 - - + -
125A PRO* 4.4 4.3 - - + -
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Residues in contact with ALA 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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40A LEU* 3.8 17.5 - - + -
44A VAL* 4.3 3.6 - - + -
88A TYR* 3.3 13.0 - - - -
89A CYS* 3.8 0.5 - - - -
90A MET* 2.9 48.0 + - + +
102A ALA* 1.3 79.2 - - - +
104A THR* 1.3 62.9 + - - +
108A GLY 3.5 7.6 - - - -
109A VAL* 4.1 17.0 - - + -
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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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44A VAL* 5.3 1.0 - - - +
88A TYR* 3.7 14.9 + - - +
103A ALA* 1.3 78.3 - - - +
105A PRO* 1.4 71.8 - - - +
106A ASP* 2.7 23.0 + - - +
107A LYS* 3.2 18.0 + - + +
108A GLY* 2.9 30.1 + - - -
110A TYR* 4.2 11.0 - - + +
124A CYS* 3.5 36.6 - - + -
125A PRO* 5.1 1.8 - - - +
24E LEU* 5.3 0.3 - - - +
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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