Contacts of the helix formed by residues 385 - 399 (chain V) 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 385 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383V ASP 4.3 6.8 + - - +
384V ALA* 1.3 72.8 - - - +
386V PRO* 1.3 67.3 - - - +
387V GLU* 3.1 24.8 - - + +
388V TYR* 3.1 8.5 + - + +
389V ILE* 3.0 22.8 + - - +
428V MET 5.2 0.8 + - - -
429V GLN* 2.7 34.9 + - - +
430V VAL 4.7 1.2 + - - -
81X ARG* 4.7 12.9 - - - +
83X LYS* 4.4 20.8 - - - +
302X ALA* 5.7 6.7 - - - +
303X THR* 5.5 2.3 + - - +
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Residues in contact with PRO 386 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371V LYS* 4.8 1.3 - - - -
384V ALA 3.7 3.7 - - - +
385V ASN* 1.3 79.3 - - + +
387V GLU* 1.3 80.4 + - - +
389V ILE* 2.9 13.1 + - + +
390V ALA* 2.7 35.9 + - - +
83X LYS* 5.1 2.9 - - - +
150X VAL* 5.0 6.5 - - + +
152X VAL* 4.0 12.3 - - + -
238X SER* 3.4 27.2 - - - +
239X ALA 3.8 10.1 - - - +
240X GLU* 3.7 33.2 - - + +
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Residues in contact with GLU 387 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385V ASN* 3.1 17.3 - - + +
386V PRO* 1.3 106.2 - - - +
388V TYR* 1.3 62.8 + - - +
390V ALA* 3.7 3.1 + - - +
391V GLU* 3.3 24.1 + - - +
429V GLN* 4.5 5.4 - - - +
81X ARG* 3.3 46.9 + - - +
83X LYS* 4.9 7.1 + - - -
150X VAL* 6.0 1.2 - - - +
152X VAL* 4.0 18.5 - - + +
158X ILE* 4.4 13.8 - - + +
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Residues in contact with TYR 388 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337V GLU* 3.6 29.6 - - + +
338V MET 3.0 17.0 + - - -
339V LEU* 3.6 2.1 - - - +
384V ALA* 5.2 1.1 - - + -
385V ASN* 3.1 11.7 + - + +
386V PRO 3.1 0.6 - - - -
387V GLU* 1.3 78.8 - - - +
389V ILE* 1.3 66.0 + - - +
391V GLU* 3.2 11.8 + - + +
392V LEU* 3.1 39.6 + - + +
429V GLN* 3.1 62.1 + - + +
430V VAL 4.1 8.3 - - - -
431V ILE* 3.6 27.6 - - + -
462V PHE* 3.2 23.8 - + - -
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Residues in contact with ILE 389 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369V PHE* 5.7 4.0 - - + -
371V LYS* 3.8 34.5 - - + -
384V ALA* 3.9 13.2 - - + +
385V ASN 3.0 16.5 + - - +
386V PRO* 2.9 11.5 + - + +
388V TYR* 1.3 74.0 - - + +
390V ALA* 1.3 68.5 + - - +
392V LEU* 3.0 13.6 + - + +
393V ARG* 2.9 23.6 + - + +
431V ILE* 3.6 23.8 - - + -
115X GLN* 4.9 2.0 - - - +
237X VAL* 3.7 36.3 - - + +
238X SER* 3.9 6.7 - - - -
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Residues in contact with ALA 390 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386V PRO 2.7 14.5 + - - +
387V GLU 3.8 3.4 - - - +
389V ILE* 1.3 72.4 - - - +
391V GLU* 1.3 65.0 + - - +
393V ARG* 2.9 19.1 + - - +
394V ARG* 2.9 13.5 + - - +
152X VAL* 3.5 31.6 - - + -
153X LYS 3.7 11.7 - - - +
154X LYS* 4.3 6.5 - - - +
156X GLY* 5.4 1.8 - - - -
238X SER* 3.5 17.8 - - - +
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Residues in contact with GLU 391 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337V GLU* 5.6 4.5 - - - +
387V GLU 3.3 12.6 + - - +
388V TYR* 3.2 18.3 + - + +
389V ILE 3.1 0.6 - - - -
390V ALA* 1.3 78.6 - - + +
392V LEU* 1.3 64.5 + - + +
394V ARG* 3.1 51.7 + - - +
395V ILE* 2.9 33.1 + - + +
465V ASN* 4.5 4.2 - - - +
154X LYS 4.4 5.5 - - - +
155X ASP 5.4 3.1 - - - +
156X GLY* 5.6 2.4 + - - -
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Residues in contact with LEU 392 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339V LEU* 4.0 7.2 - - + -
369V PHE* 3.5 26.7 - - + -
388V TYR* 3.1 30.3 + - + +
389V ILE* 3.0 7.7 + - + +
391V GLU* 1.3 77.0 - - + +
393V ARG* 1.3 57.3 + - + +
395V ILE* 3.3 10.0 + - + +
396V LEU* 2.8 40.0 + - + +
431V ILE* 3.5 38.8 - - + -
462V PHE* 3.5 36.6 - - + -
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Residues in contact with ARG 393 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389V ILE* 2.9 18.3 + - + +
390V ALA* 3.0 18.4 - - - +
392V LEU* 1.3 78.9 - - - +
394V ARG* 1.3 59.7 + - - +
396V LEU* 3.1 11.1 + - - +
397V SER* 2.7 25.2 + - - +
403V TRP* 4.3 20.2 + - + +
152X VAL 3.8 2.8 + - - -
154X LYS* 4.1 26.8 - - + +
232X SER* 5.1 0.4 + - - -
234X GLU* 2.6 47.4 + - - +
235X ASP* 2.8 40.2 + - - +
237X VAL* 4.4 11.4 - - + -
238X SER* 2.6 37.8 + - - +
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Residues in contact with ARG 394 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390V ALA 2.9 6.0 + - - +
391V GLU* 3.1 42.7 + - - +
393V ARG* 1.3 77.9 - - - +
395V ILE* 1.3 77.2 + - - +
397V SER* 3.0 18.1 + - - -
398V LYS* 3.1 9.1 + - + +
465V ASN* 3.6 27.7 + - - +
154X LYS* 3.8 40.5 - - + +
155X ASP* 5.4 6.2 + - - +
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Residues in contact with ILE 395 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100V LYS* 5.0 1.6 - - - +
391V GLU* 2.9 25.0 + - + +
392V LEU* 3.5 20.4 - - + +
394V ARG* 1.3 87.4 - - - +
396V LEU* 1.3 57.5 + - + +
397V SER 2.7 15.1 + - - -
398V LYS* 3.2 14.7 + - + +
399V GLU* 3.3 17.2 + - + +
461V ALA* 2.8 30.5 - - + +
462V PHE* 4.7 9.6 - - + -
464V ASN 4.6 8.7 - - - +
465V ASN* 3.5 26.2 - - + +
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Residues in contact with LEU 396 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367V ILE* 4.6 7.0 - - + -
369V PHE* 3.4 40.2 - - + -
392V LEU* 2.8 27.3 + - + +
393V ARG* 3.4 4.9 - - - +
395V ILE* 1.3 73.4 - - + +
397V SER* 1.3 53.3 + - - +
400V SER 2.3 27.1 - - - +
401V VAL* 3.3 24.0 - - + +
403V TRP* 4.2 21.2 + - + -
458V GLY* 3.4 39.7 - - - +
461V ALA* 4.3 8.5 - - + +
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Residues in contact with SER 397 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393V ARG 2.7 16.3 + - - -
394V ARG* 3.0 15.9 - - - -
395V ILE 2.7 0.8 + - - -
396V LEU* 1.3 81.8 + - - +
398V LYS* 1.3 67.2 + - - +
400V SER* 2.9 13.9 + - - +
403V TRP* 5.0 5.5 + - - -
154X LYS* 3.3 25.7 + - - -
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Residues in contact with LYS 398 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394V ARG* 3.1 7.8 + - + +
395V ILE* 3.8 8.7 - - + +
397V SER* 1.3 78.6 - - - +
399V GLU* 1.3 98.7 + - + +
400V SER* 2.8 11.0 + - - -
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Residues in contact with GLU 399 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395V ILE* 3.3 10.3 + - + +
398V LYS* 1.3 106.4 + - + +
400V SER* 1.3 71.8 + - - +
401V VAL* 3.5 8.7 + - + +
461V ALA* 3.6 37.3 - - + +
463V LEU* 4.9 10.6 - - + +
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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