Contacts of the strand formed by residues 445 - 448 (chain H) 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 GLU 445 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260H MET* 3.2 5.7 - - - -
261H GLY 2.9 30.2 + - - +
263H GLY* 3.3 10.4 + - - -
264H GLN* 2.7 47.3 + - + +
265H ASP* 3.0 26.1 + - - +
437H LEU* 3.9 7.4 - - + +
438H LEU 4.0 4.0 - - - +
439H ASN* 3.6 17.3 - - - +
440H MSE 3.7 4.8 - - - -
441H HIS* 3.1 23.4 + - - -
442H ALA 3.6 18.8 - - - +
444H TRP* 1.3 73.0 - - - +
446H ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 446 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E GLY 6.1 0.9 - - - -
174E VAL 6.6 0.2 - - - -
175E SER* 6.0 2.0 - - - -
200E ASN* 4.6 1.3 - - - +
252H TYR* 3.6 37.5 - - + +
258H MET* 3.6 38.4 - - + -
259H VAL 3.3 4.9 - - - +
260H MET* 4.1 20.4 - - + -
264H GLN* 4.3 0.4 - - - -
363H LEU* 5.1 1.9 - - + +
437H LEU* 3.0 19.1 - - - +
438H LEU* 3.1 46.9 + - + +
439H ASN* 4.5 10.8 - - - +
445H GLU* 1.3 81.4 - - - +
447H SER* 1.3 65.2 + - - +
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Residues in contact with SER 447 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H ASN* 5.2 0.2 + - - -
258H MET* 2.9 11.4 - - - +
259H VAL* 2.8 37.4 + - - +
264H GLN* 2.8 31.1 + - - -
268H ILE* 3.8 16.5 - - - +
363H LEU* 4.3 3.6 - - - -
435H VAL* 4.9 1.6 - - - -
436H ALA 4.4 4.5 - - - -
437H LEU* 3.5 12.1 - - - -
446H ILE* 1.3 79.2 - - - +
448H SER* 1.3 60.3 + - - +
449H LYS 3.7 0.2 + - - -
452H ILE* 3.9 5.1 - - - +
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Residues in contact with SER 448 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E ILE* 4.5 3.3 - - - +
13H TRP* 4.3 6.1 + - - -
257H SER 3.8 7.5 + - - -
258H MET* 4.3 1.6 - - - -
363H LEU* 3.4 21.9 - - - +
364H GLY* 3.8 8.4 - - - -
436H ALA 4.7 2.4 + - - -
447H SER* 1.3 73.4 - - - +
449H LYS* 1.3 66.2 + - - +
450H ALA* 3.4 16.1 + - - +
451H ASP* 2.8 42.8 + - - +
452H ILE* 2.8 15.1 + - - +
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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