Contacts of the strand formed by residues 316 - 321 (chain A) in PDB entry 1JEQ
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 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A THR* 5.6 1.1 - - + -
311A LEU* 3.7 31.4 - - + -
312A LEU 4.1 4.2 + - - -
313A PRO* 3.4 22.9 + - - +
314A SER 3.3 3.1 + - - -
315A ASP* 1.3 88.6 - - - +
317A LYS* 1.3 63.5 + - - +
318A ARG* 3.8 14.2 + - - -
330A GLU* 5.1 2.6 - - - +
331A LYS* 5.5 3.8 + - - +
278B VAL* 3.7 21.9 - - + +
279B VAL 3.1 21.3 - - - +
281B ALA* 3.8 2.0 - - - +
289B ILE* 4.5 2.0 - - + -
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Residues in contact with LYS 317 (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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314A SER 6.0 0.2 - - - +
316A THR* 1.3 76.3 - - - +
318A ARG* 1.3 72.8 + - - +
328A ILE* 3.5 29.3 - - + +
329A LEU 4.0 4.9 - - - +
330A GLU* 3.8 31.2 + - - +
331A LYS 5.4 0.4 - - - +
279B VAL* 3.1 37.1 + - + +
281B ALA* 3.4 41.5 + - + +
284B LEU* 4.4 4.7 - - + +
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Residues in contact with ARG 318 (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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313A PRO* 5.3 4.2 + - - +
316A THR* 3.8 17.5 + - - -
317A LYS* 1.3 98.3 + - - +
319A SER* 1.3 60.7 + - - +
327A ILE 3.4 0.3 - - - +
328A ILE* 3.1 10.9 - - - +
329A LEU 2.8 44.4 + - - +
331A LYS* 3.9 41.3 - - - +
334A THR* 3.6 21.1 - - + -
276B TRP* 3.7 35.0 - - + -
277B THR 3.6 4.9 - - - -
278B VAL* 3.6 34.7 - - - +
279B VAL* 4.4 0.4 - - - -
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Residues in contact with SER 319 (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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318A ARG* 1.3 76.4 - - - +
320A GLN* 1.3 73.1 + - - +
321A ILE* 4.2 5.0 - - - +
326A GLN* 3.2 36.3 + - - +
327A ILE 3.2 4.7 - - - -
328A ILE* 3.7 3.8 - - - -
275B THR 3.8 0.2 - - - +
276B TRP* 3.5 1.9 - - - -
277B THR* 2.6 53.0 + - - -
279B VAL* 3.8 15.2 - - - +
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Residues in contact with GLN 320 (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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319A SER* 1.3 79.9 + - - +
321A ILE* 1.3 65.2 + - - +
322A TYR* 2.5 39.7 + - + +
325A ARG 3.9 0.2 - - - +
326A GLN* 3.6 1.6 - - - -
327A ILE* 2.8 32.9 + - + +
272B VAL* 5.6 2.6 - - - +
274B LYS* 3.7 22.1 + - + +
275B THR 3.5 28.1 - - - +
276B TRP* 3.3 41.7 - - + +
277B THR* 5.3 1.8 - - - -
490B LEU* 5.5 4.2 - - - +
494B LEU* 3.7 13.7 - - - +
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Residues in contact with ILE 321 (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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319A SER* 4.2 5.2 - - - +
320A GLN* 1.3 79.8 - - - +
322A TYR* 1.3 62.5 + - - +
323A GLY 3.3 23.8 - - - +
324A SER* 5.0 0.7 - - - -
325A ARG 3.2 14.1 - - - +
326A GLN* 4.0 22.9 - - + +
274B LYS* 2.7 37.7 + - - +
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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