Contacts of the strand formed by residues 315 - 322 (chain C) in PDB entry 4X4R
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 PRO 315 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A ARG* 4.8 4.3 + - - -
305C PHE* 3.5 37.7 - - + +
308C LEU* 3.6 14.8 - - + -
309C GLU* 3.6 39.7 - - + +
313C PHE 3.7 0.2 - - - -
314C MET* 1.3 89.2 - - - +
316C LEU* 1.3 64.9 + - - +
317C ARG 5.6 0.2 - - - +
331C PHE* 6.2 0.9 - - + -
332C GLU 3.5 7.2 - - - +
333C CYS* 4.0 15.0 - - - -
334C GLN* 4.8 2.1 + - - -
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Residues in contact with LEU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A VAL* 4.0 10.3 - - + -
342A PHE* 4.3 3.8 - - - -
343A ARG* 2.6 58.7 + - + +
377A PHE* 4.3 13.5 - - + -
274C ARG* 4.3 2.2 - - - +
276C THR* 3.8 20.6 - - + -
305C PHE* 4.1 6.3 - - - -
315C PRO* 1.3 74.9 - - - +
317C ARG* 1.3 59.7 + - - +
332C GLU* 2.7 48.8 + - + +
334C GLN* 3.2 41.1 - - + +
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Residues in contact with ARG 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A ARG* 4.1 2.9 - - - +
368A PHE* 3.6 62.1 - - + +
369A ILE 4.5 7.1 + - - -
370A GLU* 4.4 5.4 + - - +
377A PHE* 3.7 11.8 - - + -
237C ARG* 4.6 10.7 - - - +
305C PHE* 4.1 8.8 - - - -
315C PRO* 5.6 0.3 - - - +
316C LEU* 1.3 87.2 - - + +
318C SER* 1.3 65.7 + - - +
331C PHE* 3.8 1.9 - - - +
332C GLU* 3.3 27.1 + - - +
431C GLU* 3.4 24.2 + - - +
432C MET* 3.2 46.1 + - + +
434C GLY* 5.1 1.6 - - - +
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Residues in contact with SER 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C SER* 3.3 24.4 + - - -
302C ARG* 5.6 0.9 - - - -
305C PHE* 3.9 21.9 - - - +
317C ARG* 1.3 81.7 + - - +
319C ALA* 1.3 65.8 + - - +
320C PHE* 6.0 0.2 - - - -
330C LEU 3.3 10.8 - - - -
331C PHE* 3.9 7.0 - - - -
432C MET* 3.9 5.3 - - - +
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Residues in contact with ALA 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C SER* 4.2 2.6 + - - -
318C SER* 1.3 79.7 + - - +
320C PHE* 1.3 68.4 + - - +
329C LEU* 3.5 1.6 - - - -
330C LEU* 2.5 49.6 + - + +
428C GLU* 4.7 7.6 - - + +
432C MET* 3.6 26.7 - - + -
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Residues in contact with PHE 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C TYR* 3.7 31.7 - + + -
297C LEU* 3.7 33.9 - - + -
298C GLU* 3.7 42.4 - - + -
301C SER* 4.1 9.4 - - - -
319C ALA* 1.3 82.9 - - - +
321C LYS* 1.3 61.5 + - - +
328C TYR 3.1 18.6 - - - +
329C LEU* 3.9 12.1 - - + -
330C LEU* 4.5 3.1 - - - +
428C GLU* 4.0 12.0 - - - +
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Residues in contact with LYS 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C TYR* 5.8 1.8 - - - -
297C LEU* 4.8 4.7 - - - +
320C PHE* 1.3 78.3 - - - +
322C ALA* 1.3 71.2 + - - +
323C SER* 4.0 5.8 - - - +
327C CYS* 3.5 3.3 - - - +
328C TYR* 2.9 35.9 + - + +
424C PRO* 2.9 37.5 + - + +
425C VAL* 4.5 14.1 - - + +
427C ALA* 4.9 7.1 - - - +
428C GLU* 3.3 38.8 + - + +
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Residues in contact with ALA 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C LYS* 4.6 3.7 - - + +
293C LEU* 4.0 25.4 - - + -
294C TYR* 3.8 27.8 + - + +
297C LEU* 4.3 4.5 - - + +
321C LYS* 1.3 81.2 - - - +
323C SER* 1.3 67.0 + - - +
326C PHE 3.8 4.3 - - - -
327C CYS* 4.0 10.3 - - - -
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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