Contacts of the strand formed by residues 134 - 139 (chain A) in PDB entry 5IHB
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 LEU 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 4.7 2.9 - - + +
26A GLN* 3.4 26.2 - - + +
27A GLU 3.9 0.4 - - - -
28A SER 4.4 0.4 - - - -
29A VAL* 3.8 24.0 - - + +
39A VAL* 4.0 32.1 - - + -
60A TRP* 4.1 20.0 - - + -
103A LEU* 3.8 28.9 - - + -
105A ILE* 5.8 0.4 - - + -
115A SER* 3.3 2.4 - - - -
116A TYR* 2.7 48.3 + - + +
133A GLN* 1.3 71.6 - - - +
135A SER* 1.3 61.6 + - - +
136A VAL* 4.4 12.6 - - + -
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Residues in contact with SER 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU 2.8 19.5 + - - -
28A SER* 3.3 3.7 - - - -
29A VAL* 2.8 33.3 + - - +
114A GLY* 3.4 8.5 + - - -
115A SER* 4.1 14.1 + - - +
133A GLN 3.8 0.6 + - - -
134A LEU* 1.3 72.3 - - - +
136A VAL* 1.3 57.7 + - - +
137A HIS* 3.2 25.1 + - - -
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Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 3.5 22.0 - - + +
31A VAL* 4.5 8.7 - - + -
90A PHE* 5.6 0.2 - - + -
103A LEU* 6.0 0.2 - - + -
105A ILE* 4.3 20.9 - - + -
112A ASP* 3.8 24.5 - - + +
113A ASN* 3.4 6.4 - - - +
114A GLY* 2.9 25.7 + - - +
116A TYR* 3.6 24.7 - - + -
134A LEU* 4.4 8.7 - - + -
135A SER* 1.3 76.4 + - - +
137A HIS* 1.3 69.5 + - - +
138A VAL* 4.2 17.9 - - + -
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Residues in contact with HIS 137 (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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28A SER* 3.5 26.0 + - - -
29A VAL 2.8 10.9 + - - +
30A THR* 3.3 20.9 - - + +
31A VAL* 3.0 27.9 + - - +
113A ASN* 3.7 4.1 + - - -
135A SER* 3.2 24.2 + - - -
136A VAL* 1.3 78.9 + - - +
138A VAL* 1.3 62.6 + - - +
139A THR* 4.1 4.0 - - + -
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Residues in contact with VAL 138 (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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31A VAL* 3.2 21.8 - - + +
32A GLN 4.4 0.4 - - - -
33A GLU* 3.8 27.6 - - + +
108A ALA* 4.7 4.3 - - + -
109A ARG 3.3 29.2 - - - +
110A ARG* 3.5 29.8 + - + +
112A ASP* 4.2 5.6 - - + -
113A ASN* 2.9 26.7 + - - +
136A VAL* 4.2 11.7 - - + -
137A HIS* 1.3 76.4 - - - +
139A THR* 1.3 63.6 + - - +
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Residues in contact with THR 139 (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 THR* 3.8 25.9 - - + +
31A VAL 3.1 5.6 + - - -
32A GLN* 3.3 22.7 + - - +
33A GLU* 2.7 30.7 + - - +
110A ARG* 4.2 7.0 - - - +
137A HIS* 4.8 4.9 - - + +
138A VAL* 1.3 77.6 - - - +
140A ASP* 1.3 61.1 + - - +
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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