Contacts of the strand formed by residues 96 - 101 (chain A) in PDB entry 1X4B
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 ARG 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLY* 3.3 38.7 - - - -
35A LEU 4.6 0.7 - - - -
36A SER* 3.6 37.3 - - - +
37A PHE* 5.2 8.3 - - - -
92A SER* 3.1 6.9 - - - -
93A ILE 2.8 42.1 + - - +
94A ASP 4.6 2.0 - - - +
95A GLY* 1.3 81.7 - - - +
97A VAL* 1.3 82.3 + - - +
98A VAL* 3.5 4.0 - - + -
99A GLU* 4.0 6.1 + - - -
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Residues in contact with VAL 97 (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 PRO* 4.7 15.5 - - + -
91A HIS 3.6 6.7 - - - +
92A SER* 4.6 6.3 - - - +
96A ARG* 1.3 97.2 + - - +
98A VAL* 1.3 69.1 + - - +
99A GLU* 3.6 6.7 - - - +
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 4.5 4.9 - - + -
33A GLY 3.7 3.4 - - - +
34A GLY 2.9 28.9 - - - +
35A LEU* 4.7 4.5 - - + -
48A TYR* 4.3 7.9 - - - +
89A ARG* 6.1 0.2 - - - -
90A PRO* 5.2 1.4 - - - +
91A HIS* 2.7 42.7 + - + +
93A ILE* 3.9 31.4 - - + +
96A ARG* 3.5 23.1 - - + +
97A VAL* 1.3 83.3 - - - +
99A GLU* 1.3 75.5 + - - +
100A PRO* 4.5 0.2 - - - +
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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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33A GLY* 2.9 41.3 + - - +
34A GLY* 4.5 1.9 - - - -
89A ARG* 5.5 2.2 - - - +
96A ARG* 4.0 8.3 + - - -
97A VAL* 3.6 12.2 - - - +
98A VAL* 1.3 90.2 - - - +
100A PRO* 1.4 73.6 - - + +
101A LYS* 3.6 10.8 - - + +
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Residues in contact with PRO 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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30A LEU* 5.2 8.3 - - + -
31A PHE 3.8 4.5 - - - +
32A ILE* 3.9 13.9 - - + -
48A TYR* 3.5 17.4 - - + +
85A ALA 5.0 5.2 - - - +
86A MET* 5.8 4.7 - - + +
89A ARG* 4.0 30.9 - - + +
91A HIS* 3.5 33.0 - - + +
98A VAL 4.4 0.7 - - - +
99A GLU* 1.4 84.7 - - - +
101A LYS* 1.3 71.5 + - - +
102A ARG* 3.4 14.3 + - - +
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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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30A LEU* 3.2 12.6 - - - +
31A PHE* 2.6 70.6 + - + +
33A GLY* 4.7 3.1 - - - +
86A MET* 4.8 1.3 - - - -
99A GLU* 3.6 15.7 - - - +
100A PRO* 1.3 83.1 - - - +
102A ARG* 1.3 70.2 + - - +
103A ALA 4.1 2.5 - - - +
106A ARG* 6.1 4.8 - - + +
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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