Contacts of the strand formed by residues 350 - 356 (chain A) in PDB entry 2GLQ
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 THR 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ASN* 3.0 29.9 + - + +
37A ILE* 3.9 22.0 - - + -
345A THR* 3.8 17.0 - - + +
346A SER 3.0 14.5 + - - -
347A GLU* 4.0 6.2 - - - -
349A ASP* 1.3 88.4 + - - +
351A LEU* 1.3 64.0 + - - +
352A SER* 3.7 19.8 + - - +
442A ARG* 3.6 2.1 - - - +
443A GLY* 3.5 9.0 - - - -
444A PRO* 3.3 13.1 - - - +
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA* 4.0 6.2 - - + +
35A ASN 3.0 7.1 + - - -
36A LEU* 3.5 22.0 - - + +
37A ILE 2.9 25.3 + - - +
350A THR* 1.3 71.7 - - - +
352A SER* 1.3 60.0 + - - +
353A LEU* 3.8 25.1 - - + -
442A ARG 3.5 16.4 - - - +
444A PRO* 3.5 23.3 - - - +
445A GLN* 5.1 0.9 - - + -
446A ALA* 3.8 21.5 - - + -
449A VAL* 5.8 0.2 - - + -
461A VAL* 4.2 15.5 - - + +
462A MET* 4.2 7.8 - - + +
465A ALA* 3.4 29.2 - - + -
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Residues in contact with SER 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.4 14.1 - - - +
39A PHE* 4.0 15.4 - - - -
74A PHE* 3.7 19.8 - - - -
345A THR* 5.0 2.4 + - - -
350A THR* 3.7 17.7 + - - +
351A LEU* 1.3 75.5 + - - +
353A LEU* 1.3 63.1 + - - +
441A ALA* 3.3 4.0 - - - -
442A ARG* 2.9 43.3 + - - +
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Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE 3.0 9.1 + - - +
38A ILE* 3.4 10.8 - - + +
39A PHE* 2.8 34.8 + - - +
351A LEU* 3.8 22.7 - - + -
352A SER* 1.3 82.0 - - - +
354A VAL* 1.3 56.6 + - - +
355A THR* 5.8 0.9 - - + -
439A VAL* 4.1 8.3 - - + -
440A PHE 3.2 4.7 - - - +
441A ALA* 3.4 20.9 - - + -
449A VAL* 4.3 6.1 - - + -
458A ILE* 3.8 42.8 - - + +
461A VAL* 3.9 18.8 - - + -
462A MET* 4.3 13.0 - - + -
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Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A PHE* 3.3 17.3 - - + +
44A MET* 4.2 10.1 - - + -
71A MET* 4.3 8.5 - - + -
74A PHE* 3.7 28.9 - - + -
334A PHE* 4.0 11.9 - - + -
338A ILE* 3.7 34.3 - - + -
353A LEU* 1.3 72.8 - - - +
355A THR* 1.3 68.1 + - - +
439A VAL* 3.4 1.4 - - - +
440A PHE* 2.8 53.8 + - + +
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Residues in contact with THR 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 4.5 15.5 - - + -
39A PHE 2.9 10.9 + - - +
40A LEU* 3.5 19.0 - - + -
41A GLY* 2.8 25.5 + - - -
44A MET* 4.3 10.4 - - - +
80A SER* 4.8 1.7 + - - -
99A TYR* 5.2 4.3 - - + -
353A LEU* 5.5 1.6 - - + -
354A VAL* 1.3 80.0 - - - +
356A ALA* 1.3 72.9 + - - +
437A VAL* 4.1 3.5 - - - +
438A ALA 2.8 19.2 + - - -
439A VAL* 3.6 19.2 - - + +
440A PHE* 5.3 0.2 - - - -
455A GLN* 6.0 0.4 - - + +
458A ILE* 4.8 14.4 - - + +
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Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.9 6.2 - - - +
41A GLY 3.2 18.2 - - - +
44A MET* 3.2 34.3 - - + +
99A TYR* 5.2 0.2 - - - -
355A THR* 1.3 83.9 + - - +
357A ASP* 1.3 63.4 + - - +
358A HIS 3.8 7.6 - - - +
437A VAL* 3.4 23.8 - - + +
438A ALA 3.9 3.2 + - - +
455A GLN* 3.6 6.4 - - - +
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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