Contacts of the strand formed by residues 129 - 133 (chain N) in PDB entry 5A0Q
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 GLY 129 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M GLY* 3.9 11.9 - - - +
62M LEU* 4.4 0.3 - - - +
93N THR* 3.4 24.1 - - - +
96N MET* 4.0 14.3 - - - +
97N TYR* 4.3 14.5 - - - -
125N VAL* 4.8 2.0 - - - -
126N ASP 3.0 12.0 + - - -
127N MET 3.1 3.2 + - - -
128N LEU* 1.4 76.0 - - - +
130N VAL* 1.4 64.5 + - - +
131N ALA* 3.7 0.7 + - - +
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Residues in contact with VAL 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M ASN* 5.4 3.8 - - - +
29M LEU* 4.2 24.0 - - + -
31M GLU* 5.8 8.1 - - + -
57M PHE* 3.5 32.5 - - + -
58M HIS* 4.1 17.3 - - + +
59M GLY* 3.6 16.8 - - - +
124N TYR* 3.9 3.0 - - + +
125N VAL* 3.7 1.9 - - - -
126N ASP* 3.0 47.4 + - + +
128N LEU 3.5 0.2 - - - -
129N GLY* 1.4 73.9 - - - +
131N ALA* 1.4 63.5 + - - +
132N TYR* 4.5 8.5 - - + -
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Residues in contact with ALA 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58M HIS* 3.1 25.1 - - - -
62M LEU* 3.6 25.1 - - + +
89N HIS* 3.1 26.5 - - + +
93N THR* 3.2 20.6 - - + +
124N TYR 3.5 4.7 - - - -
125N VAL* 4.8 0.7 - - + -
130N VAL* 1.4 79.5 - - - +
132N TYR* 1.3 62.7 + - - +
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Residues in contact with TYR 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29M LEU* 3.8 21.3 - - + -
36M HIS* 2.5 51.6 + + + +
37M THR* 3.5 27.8 - - + -
39M ASP 5.4 0.4 - - - +
40M SER* 4.6 4.0 - - - +
58M HIS* 4.7 4.3 - - + -
89N HIS* 3.9 8.2 - - - -
123N GLY* 3.6 0.3 - - - -
124N TYR* 2.9 56.2 + + - +
130N VAL* 4.5 3.1 - - + -
131N ALA* 1.3 78.9 - - - +
133N GLU* 1.3 74.0 + - - +
134N ALA* 3.6 18.8 - - + -
137N LEU* 3.6 16.7 - - + +
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Residues in contact with GLU 133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37M THR* 3.8 8.1 + - - +
39M ASP* 4.8 4.7 - - - +
15N LYS* 3.2 26.4 + - - -
86N ARG* 5.3 1.1 - - - +
119N GLU* 5.0 4.0 - - - +
121N PHE* 3.5 40.1 - - + -
122N LEU 3.5 13.6 + - - +
123N GLY* 4.1 3.1 - - - -
132N TYR* 1.3 82.1 - - - +
134N ALA* 1.3 79.7 + - - +
135N PRO* 3.2 6.5 - - - +
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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