Contacts of the strand formed by residues 140 - 145 (chain Z) in PDB entry 5GGR
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 ALA 140 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37Z PHE* 3.6 35.7 - - + +
39Z PRO 3.9 9.6 - - - +
40Z ALA* 3.7 17.0 - - - +
52Z PHE* 4.2 4.9 - - + -
120Z THR* 3.3 4.2 - - - -
121Z TYR* 2.4 42.7 + - - +
138Z LEU 3.1 2.4 + - - +
139Z ARG* 1.3 74.2 - - - +
141Z GLU* 1.3 58.9 + - - +
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Residues in contact with GLU 141 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40Z ALA 3.6 5.3 + - - -
41Z LEU* 3.1 35.2 - - + +
42Z LEU 3.4 18.7 + - - -
52Z PHE* 3.5 11.0 - - - -
119Z GLY* 3.5 17.7 - - - +
120Z THR* 4.3 8.7 - - - +
121Z TYR* 5.1 0.4 - - - -
140Z ALA* 1.3 75.6 - - - +
142Z LEU* 1.3 69.3 + - - +
143Z ARG* 3.2 27.9 - - - +
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Residues in contact with LEU 142 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42Z LEU* 3.2 31.2 - - + +
44Z VAL* 4.3 6.1 - - + -
50Z ALA* 3.7 30.7 - - + -
52Z PHE* 4.1 13.0 - - + -
110Z VAL* 5.4 9.9 - - + -
113Z ALA* 5.9 2.2 - - + -
117Z ASP* 4.8 8.7 - - + +
118Z SER* 3.6 16.9 + - - +
119Z GLY 3.1 10.3 + - - +
121Z TYR* 4.1 31.4 - - + +
141Z GLU* 1.3 80.0 - - - +
143Z ARG* 1.3 70.1 + - - +
144Z VAL* 3.9 20.4 - - + -
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Residues in contact with ARG 143 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Z LEU* 3.5 16.3 - - + +
42Z LEU 2.7 14.4 + - - +
43Z VAL* 3.2 20.4 - - + +
44Z VAL 2.8 27.0 + - - +
118Z SER* 3.9 1.6 - - - -
141Z GLU* 3.2 26.5 - - - +
142Z LEU* 1.3 73.8 - - - +
144Z VAL* 1.3 63.8 + - - +
145Z THR* 4.6 17.6 - - + +
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Residues in contact with VAL 144 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Z VAL* 3.0 30.7 - - + +
46Z GLU* 4.7 6.7 - - + +
113Z ALA* 4.5 5.4 - - + -
114Z ARG 3.0 28.7 - - - +
115Z ARG* 3.3 30.0 + - + +
117Z ASP* 5.4 0.9 - - + -
118Z SER* 2.9 29.6 + - - +
142Z LEU* 3.9 18.8 - - + -
143Z ARG* 1.3 76.6 + - - +
145Z THR* 1.3 64.6 + - - +
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Residues in contact with THR 145 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43Z VAL* 4.7 15.7 - - + +
44Z VAL 3.0 14.5 + - - +
45Z THR* 3.4 16.5 - - - +
46Z GLU* 3.1 25.7 + - - +
115Z ARG* 3.7 15.7 + - - +
143Z ARG* 4.6 20.6 - - - +
144Z VAL* 1.3 79.3 - - - +
146Z GLU* 1.3 71.4 + - - +
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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