Contacts of the strand formed by residues 319 - 324 (chain E) in PDB entry 1QRP
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 GLN 319 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E TRP* 3.7 47.7 + - + +
182E VAL 3.2 12.6 - - - +
183E PRO* 4.2 13.0 - - + +
184E VAL* 4.2 3.5 - - - +
190E TRP* 3.8 2.6 - - - -
314E ASP* 2.9 40.9 + - + +
317E ASN* 3.6 28.1 - - - +
318E ASN* 1.3 80.4 - - - +
320E VAL* 1.3 61.0 + - - +
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Residues in contact with VAL 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E ASN 3.6 1.4 - - - +
181E TRP* 3.5 4.2 - - - -
182E VAL* 2.8 45.8 + - + +
184E VAL* 4.2 4.0 - - + -
190E TRP* 3.8 32.8 - - + -
192E ILE* 4.2 22.7 - - + -
214E VAL* 4.3 12.8 - - + -
311E THR* 3.7 28.0 - - + -
312E VAL 3.3 4.3 - - - +
313E PHE* 4.5 4.3 - - + -
319E GLN* 1.3 74.8 - - - +
321E GLY* 1.3 61.8 + - - +
322E LEU* 4.2 15.3 - - + -
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Residues in contact with GLY 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E LEU* 3.9 9.9 - - - -
180E ASN 3.3 7.2 - - - -
181E TRP* 3.6 22.9 - - - -
310E PHE 3.5 0.2 - - - +
311E THR* 3.3 7.4 - - - +
312E VAL* 2.7 40.8 + - - +
320E VAL* 1.3 71.9 - - - +
322E LEU* 1.3 63.8 + - - +
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Residues in contact with LEU 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E LEU* 3.9 3.5 - - - +
180E ASN* 2.9 39.1 + - - +
182E VAL* 4.4 14.4 - - + -
192E ILE* 5.3 4.3 - - + -
214E VAL* 5.5 3.8 - - + -
262E ILE* 4.2 17.5 - - + -
267E TYR* 3.7 41.1 - - + +
305E PHE* 4.1 22.0 - - + -
309E TYR* 4.2 7.4 - - + -
310E PHE 3.5 2.7 - - - +
311E THR* 3.7 29.4 - - + +
320E VAL* 4.2 11.0 - - + -
321E GLY* 1.3 78.1 - - - +
323E ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E TYR* 3.6 35.9 - - + -
176E THR 3.9 3.8 - - - +
178E SER 4.0 11.0 - - - +
179E LEU* 4.1 7.2 - - + -
180E ASN* 4.9 0.7 - - - +
267E TYR* 5.4 0.2 - - - -
309E TYR* 3.3 7.4 - - - -
310E PHE* 2.9 32.9 + - - +
322E LEU* 1.3 76.4 - - - +
324E PRO* 1.3 73.4 - - + +
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Residues in contact with PRO 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E TYR* 3.2 2.8 - - - -
176E THR* 2.9 52.8 + - + +
178E SER 5.6 1.1 - - - +
180E ASN* 5.4 5.2 - - - +
267E TYR* 5.7 2.0 - - + -
308E GLN 3.6 9.4 - - - +
309E TYR* 3.6 21.1 - - + -
323E ALA* 1.3 85.3 - - + +
325E VAL* 1.3 65.5 + - - +
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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