Contacts of the helix formed by residues 11 - 16 (chain P) in PDB entry 2GLJ
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 ASN 11 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123M ASP* 6.0 4.6 - - - +
204M GLY* 4.6 4.0 - - - -
206M ILE* 3.8 24.5 - - + +
10P LYS* 1.3 81.0 + - - +
12P ALA* 1.3 55.9 + - - +
13P TRP* 2.4 66.0 + - - +
14P ASP* 3.6 14.0 + - - +
15P LYS* 4.5 3.6 + - - +
363P LEU 4.4 7.9 + - - -
364P GLY* 3.6 18.7 + - - -
365P LYS* 4.8 11.0 - - - +
402P ASN* 4.5 3.9 + - - -
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Residues in contact with ALA 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P LYS 4.3 0.8 + - - -
11P ASN* 1.3 69.1 - - - +
13P TRP* 1.3 64.3 + - + +
15P LYS* 3.6 9.4 - - - +
16P TYR* 3.3 22.6 + - + +
364P GLY 2.9 24.4 + - - +
365P LYS* 4.5 1.6 - - - +
366P GLY 4.4 7.0 - - - +
402P ASN* 4.3 11.2 - - - +
450P ALA* 3.6 24.5 - - + -
454P GLU* 3.6 21.8 - - - +
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Residues in contact with TRP 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203M ILE* 5.0 1.2 - - - +
204M GLY* 3.9 7.9 - - - +
205M SER* 3.7 36.7 - - - +
206M ILE 5.1 2.5 - - - +
11P ASN* 2.4 55.0 + - - +
12P ALA* 1.3 74.0 - - + +
14P ASP* 1.3 63.9 + - - +
15P LYS 2.5 17.9 + - - -
16P TYR* 3.8 10.8 - + - -
22P LYS* 4.7 21.3 - - + -
25P PHE* 3.3 39.7 - + - -
26P ALA* 5.7 4.0 - - + -
256P ARG 5.6 0.2 - - - -
257P SER* 3.9 34.1 - - - -
364P GLY* 4.9 3.6 - - - -
448P SER* 4.3 6.5 + - - -
449P LYS* 4.5 2.7 - - + -
450P ALA* 3.4 31.0 - - + +
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Residues in contact with ASP 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206M ILE* 2.9 28.4 - - - +
207M PRO* 4.7 0.5 - - - +
210M ASP* 4.1 19.1 - - - +
216M LYS* 5.8 2.4 + - - -
10P LYS* 6.1 2.9 - - - +
11P ASN* 3.6 22.3 + - - +
13P TRP* 1.3 79.7 - - - +
15P LYS* 1.3 65.8 + - - +
16P TYR* 3.0 3.7 + - - +
17P ASP* 3.6 29.5 + - - +
22P LYS* 5.6 1.0 - - - +
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Residues in contact with LYS 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P LYS* 5.0 13.9 - - - +
11P ASN 4.6 2.7 - - - +
12P ALA 3.6 14.4 - - - +
13P TRP 2.5 9.3 + - - +
14P ASP* 1.3 74.6 - - - +
16P TYR* 1.3 84.7 + - + +
21P LEU* 3.9 13.4 - - + +
400P SER* 3.7 21.8 + - - -
401P VAL 4.4 1.4 - - - +
402P ASN* 3.4 21.4 + - - +
453P TYR* 5.3 1.2 - - - -
454P GLU* 2.8 29.1 + - - -
457P ASN* 5.4 0.8 - - - +
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Residues in contact with TYR 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P ALA* 3.3 18.9 + - + +
13P TRP* 3.8 12.8 - + - -
14P ASP 3.0 0.8 - - - -
15P LYS* 1.3 104.9 - - + +
17P ASP* 1.3 73.9 + - - +
18P ASP* 2.7 14.4 + - - +
21P LEU* 3.2 18.1 - - + +
22P LYS* 4.3 9.6 - - + -
25P PHE* 3.4 23.1 - + - -
450P ALA* 2.9 40.8 + - + -
453P TYR* 3.0 36.1 - + - -
454P GLU* 2.5 34.7 + - - -
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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