Contacts of the strand formed by residues 421 - 425 (chain H) in PDB entry 1QGN
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 421 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212H PRO* 3.8 18.4 - - + -
213H PHE* 3.4 41.5 - - + -
338H TYR* 4.2 8.7 - - + -
363H SER* 4.1 15.0 - - - -
364H PHE 3.8 11.2 - - - +
365H GLU* 4.4 7.5 - - + +
398H GLN* 3.4 21.5 - - - +
399H PRO* 3.6 22.9 - - + +
416H GLY 4.7 0.4 - - - +
417H ILE* 4.2 14.1 - - + -
418H MET* 3.1 20.7 + - + +
420H ASN* 1.3 78.5 - - - +
422H VAL* 1.3 74.9 + - - +
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Residues in contact with VAL 422 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362H VAL 4.2 0.2 - - - +
363H SER* 3.2 6.2 - - - -
364H PHE* 2.9 60.3 + - + +
366H VAL* 4.6 3.6 - - + -
373H THR* 3.3 32.8 - - + -
376H PHE* 4.4 16.8 - - + -
377H VAL* 4.6 6.1 - - + -
396H VAL* 3.9 24.9 - - + -
397H ASP 3.8 6.7 - - - +
398H GLN* 4.5 4.9 - - + -
399H PRO* 4.4 1.3 - - - -
420H ASN 3.6 2.7 - - - +
421H LEU* 1.3 75.3 - - - +
423H ARG* 1.3 65.7 - - - +
424H PHE 4.1 0.4 + - - -
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Residues in contact with ARG 423 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163H TYR* 5.7 3.4 - - - -
211H ASN* 3.1 35.5 + - - +
212H PRO* 4.2 10.9 - - + +
239H PHE* 4.5 2.5 - - - -
361H ALA* 5.1 11.0 - - - -
362H VAL 3.9 2.2 - - - +
363H SER* 3.2 21.5 - - - +
387H PRO* 5.2 0.4 - - - +
388H SER 4.0 24.5 + - - +
389H PHE* 4.0 26.3 - - - +
395H ILE* 3.9 1.7 - - - +
396H VAL* 3.5 5.7 - - - +
397H ASP* 3.0 68.8 + - - +
399H PRO* 4.0 11.8 - - + +
422H VAL* 1.3 75.8 - - - +
424H PHE* 1.3 67.8 - - - +
425H SER* 4.1 2.1 + - - +
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Residues in contact with PHE 424 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360H GLY 3.9 0.2 - - - +
361H ALA* 3.4 3.0 - - - +
362H VAL 2.8 45.8 + - - +
364H PHE* 4.1 21.3 - + + -
376H PHE* 5.6 0.9 - + - -
380H LEU* 3.9 16.8 - - + -
383H PRO* 3.8 20.9 - - + -
394H SER* 4.3 8.5 - - - -
395H ILE 3.8 1.8 - - - -
396H VAL* 3.4 27.4 - - + -
422H VAL 4.1 0.2 - - - -
423H ARG* 1.3 77.0 - - - +
425H SER* 1.3 74.9 + - - +
426H PHE* 3.4 44.6 + + + -
434H LEU* 5.0 6.1 - - + -
438H ILE* 4.0 27.4 - - + -
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Residues in contact with SER 425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262H PHE* 5.4 0.9 - - - -
317H GLN* 4.9 0.5 + - - -
360H GLY 3.8 6.6 + - - -
361H ALA* 4.5 4.2 - - - +
388H SER 4.6 0.7 - - - -
389H PHE* 3.0 37.5 - - - +
390H GLY* 3.1 14.6 + - - -
391H GLY 4.8 1.2 + - - -
393H GLU 4.7 1.9 + - - +
394H SER* 3.5 3.8 - - - -
395H ILE* 2.9 41.2 + - - +
423H ARG* 4.1 4.2 + - - +
424H PHE* 1.3 73.4 - - - +
426H PHE* 1.3 65.0 + - - +
427H GLY 3.4 2.3 + - - -
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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