Contacts of the strand formed by residues 100 - 104 (chain A) in PDB entry 7EHI
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 GLN 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A SER* 5.4 0.4 + - - -
39A GLU* 5.6 2.8 + - - -
92A LEU* 4.5 20.8 - - + +
93A VAL 3.3 7.6 - - - +
94A THR* 2.8 29.4 + - + +
98A GLY 3.5 4.2 + - - +
99A ILE* 1.3 76.5 - - - +
101A LYS* 1.3 76.6 + - - +
109A PHE 4.8 0.2 - - - +
110A LYS* 4.9 8.0 - - - +
111A VAL* 4.5 19.1 + - + +
604A MES 5.3 3.8 - - - +
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Residues in contact with LYS 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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4A LEU* 4.6 22.0 - - + -
92A LEU* 3.5 8.3 - - - +
93A VAL* 2.9 44.9 + - + +
99A ILE* 4.2 22.2 + - + +
100A GLN* 1.3 80.4 + - - +
102A ILE* 1.3 65.1 + - - +
108A PHE* 4.6 20.0 - - + -
109A PHE 3.4 17.0 - - - +
110A LYS* 4.2 28.6 - - - +
111A VAL* 5.1 1.6 - - - +
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Residues in contact with ILE 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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41A LEU* 3.7 22.9 - - + -
90A ALA* 3.9 14.4 - - + -
91A PHE 3.2 9.9 - - - +
92A LEU* 3.6 12.1 - - + +
101A LYS* 1.3 74.5 - - - +
103A TYR* 1.3 62.4 + - - +
104A SER 4.2 0.2 - - - -
107A GLY 3.5 1.6 - - - +
108A PHE* 3.3 5.0 - - - +
109A PHE* 2.8 62.9 + - + +
110A LYS 4.3 4.3 - - - +
111A VAL* 4.5 4.8 - - + +
114A ALA* 3.7 13.7 - - + -
116A LEU* 3.6 31.2 - - + -
121A PHE* 3.7 16.8 - - + -
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Residues in contact with TYR 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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7A ILE* 3.8 17.3 + - + -
8A MET* 3.5 22.1 - - + +
9A HIS* 3.0 41.9 + - + -
28A LEU* 3.7 19.5 - - + -
90A ALA* 3.5 3.1 - - - +
91A PHE* 2.8 52.7 + + + +
93A VAL* 4.8 8.1 - - + -
102A ILE* 1.3 72.5 - - - +
104A SER* 1.3 73.0 - - - +
107A GLY* 3.3 11.0 - - - -
108A PHE* 3.4 43.3 - + + -
123A PHE* 3.9 9.4 - + - -
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Residues in contact with SER 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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90A ALA* 3.8 9.4 - - - -
103A TYR* 1.3 80.3 - - - +
105A ASP* 1.3 64.6 - - - +
106A LYS* 3.0 10.4 + - - +
107A GLY* 2.9 21.1 + - - +
121A PHE* 2.9 56.7 + - - -
122A TYR* 4.4 1.8 - - - -
123A PHE* 3.4 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