Contacts of the strand formed by residues 12 - 16 (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 LEU 12 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10N SER 3.8 7.0 - - - +
11N VAL* 1.3 81.7 - - - +
13N GLY* 1.3 60.8 + - - +
14N VAL* 6.1 0.2 - - + -
22N ILE* 3.1 26.0 - - - +
23N ALA 3.0 19.2 + - - +
111N VAL* 5.0 2.6 - - - +
137N LEU 3.7 4.5 - - - +
138N ALA* 3.5 26.7 - - + -
142N GLY* 4.8 5.8 - - - -
146N ALA* 3.9 10.8 - - + -
150N LEU* 5.5 5.8 - - + -
169N VAL* 4.4 17.3 - - + -
172N CYS* 4.1 28.9 - - + +
173N MET* 3.6 35.0 - - + +
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Residues in contact with GLY 13 (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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12N LEU* 1.3 76.6 - - - +
14N VAL* 1.3 70.5 + - - +
21N VAL* 3.6 10.1 - - - -
22N ILE* 4.0 6.5 - - - -
111N VAL* 4.4 6.5 - - - +
122N LEU* 3.7 15.3 - - - -
136N SER 3.8 0.3 - - - -
137N LEU* 2.7 30.4 + - - +
150N LEU* 4.7 2.3 - - - +
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Residues in contact with VAL 14 (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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13N GLY* 1.3 79.5 - - - +
15N LYS* 1.4 65.8 + - + +
16N PHE* 4.0 0.2 - - - -
20N VAL* 4.0 4.7 - - - -
21N VAL* 2.8 31.4 + - + +
122N LEU* 3.5 3.4 - - - +
135N PRO* 3.4 11.0 - - + +
136N SER* 3.2 27.8 - - - +
150N LEU* 4.0 13.7 - - + -
160N LEU* 3.5 24.9 - - + -
165N ALA* 4.0 11.4 - - + +
168N LEU* 5.4 0.2 - - + -
169N VAL* 3.4 30.5 - - + -
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Residues in contact with LYS 15 (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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14N VAL* 1.4 78.5 - - + +
16N PHE* 1.3 62.4 + - - +
17N GLU* 5.0 10.1 - - - +
19N GLY 3.6 4.3 - - - +
20N VAL* 4.0 5.8 - - + +
119N GLU* 4.7 2.4 + - - -
120N SER* 3.0 49.6 + - - +
122N LEU* 3.8 9.6 - - - +
133N GLU* 3.2 24.9 + - - -
135N PRO* 3.4 35.2 + - + +
160N LEU* 3.8 13.5 - - + +
165N ALA* 3.1 17.3 - - - +
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Residues in contact with PHE 16 (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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14N VAL 4.1 0.2 - - - -
15N LYS* 1.3 72.9 - - - +
17N GLU* 1.3 56.6 + - - +
18N GLY 2.8 4.6 + - - -
19N GLY* 2.2 47.6 + - - +
20N VAL 4.2 1.1 - - - -
21N VAL* 2.4 57.2 - - + -
120N SER* 3.9 3.3 + - - -
160N LEU 4.1 1.8 - - - -
161N SER 2.6 17.9 - - - -
162N GLN* 2.5 36.3 - - + -
165N ALA* 2.1 31.6 - - + -
166N ARG* 1.7 49.8 - - + -
191N THR* 5.4 0.4 - - + -
192N VAL 5.8 0.4 - - - -
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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