Contacts of the strand formed by residues 325 - 333 (chain A) in PDB entry 4Z1H
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 325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A HIS* 4.7 5.2 - - + +
312A GLU* 4.3 15.9 - - + -
315A TYR* 3.8 20.6 - - + -
324A LYS* 1.3 90.7 - - + +
326A ARG* 1.3 62.3 + - - +
327A TYR* 3.5 20.2 + - - +
328A THR* 3.9 8.2 + - - +
344A TYR* 3.6 33.9 - - + -
345A VAL 3.4 6.7 - - - +
346A PRO* 4.2 1.8 - - + -
347A ASP* 4.4 1.6 - - - +
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Residues in contact with ARG 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LYS 3.6 3.4 + - - -
325A PRO* 1.3 68.2 - - - +
327A TYR* 1.3 83.4 + - + +
345A VAL* 2.4 37.8 + - + +
346A PRO 2.7 12.8 + - - +
347A ASP* 2.7 48.5 + - - +
348A MET 3.2 15.4 + - - -
349A LYS* 4.4 0.4 - - - +
436A LYS* 3.2 37.2 + - - +
439A LYS* 3.6 18.6 - - - +
440A PHE* 3.7 21.1 - - - +
443A ASP* 2.8 31.3 + - - +
444A TYR* 3.8 10.9 - - - -
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Residues in contact with TYR 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A PRO* 3.2 4.6 - - - +
326A ARG* 1.3 100.5 - - + +
328A THR* 1.3 64.0 + - - +
343A PHE 4.2 1.1 - - - -
344A TYR* 3.2 7.3 - - - -
345A VAL* 2.9 46.0 + - + -
425A PHE* 4.1 15.0 - + + -
426A PHE* 4.1 13.9 - + - -
429A GLN* 3.4 42.9 + - + +
433A ASP* 4.9 0.7 + - - +
436A LYS* 3.7 27.7 - - + +
437A TYR* 3.6 32.9 + + - +
440A PHE* 3.8 30.1 - + + -
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Residues in contact with THR 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A HIS* 3.7 39.0 - - + +
325A PRO* 3.9 9.5 + - - +
327A TYR* 1.3 74.6 + - - +
329A LEU* 1.3 68.9 + - - +
330A HIS* 4.2 2.8 + - + +
342A ILE* 4.5 0.4 - - + -
343A PHE 3.3 3.6 - - - +
344A TYR* 3.2 25.5 - - + -
425A PHE* 3.7 15.6 - - - -
429A GLN* 5.5 0.2 + - - -
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Residues in contact with LEU 329 (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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327A TYR 4.4 0.2 - - - -
328A THR* 1.3 74.8 - - - +
330A HIS* 1.3 70.5 + - - +
331A TYR* 3.9 10.0 + - + +
341A SER 3.8 0.3 - - - +
342A ILE* 3.3 6.6 - - - +
343A PHE* 2.9 50.9 + - + +
421A ARG* 3.8 47.1 - - + +
422A LEU* 3.9 22.2 - - + -
425A PHE* 3.8 36.7 - - + -
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Residues in contact with HIS 330 (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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298A ILE 3.5 20.6 - - - -
299A TRP* 3.2 25.8 + - - -
301A MET 3.5 15.9 + - - -
303A PRO* 3.4 40.8 + - + +
306A VAL* 4.0 11.3 - - + +
311A HIS* 4.5 11.2 - - + +
328A THR* 4.2 3.4 + - + +
329A LEU* 1.3 79.5 - - - +
331A TYR* 1.3 58.4 + - - +
332A LYS* 3.8 13.8 + - + +
341A SER 3.4 14.8 - - - -
342A ILE* 3.8 15.6 - - + +
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Residues in contact with TYR 331 (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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329A LEU* 3.8 17.4 - - + -
330A HIS* 1.3 70.5 - - - +
332A LYS* 1.3 65.4 + - - +
333A THR* 3.3 39.9 + - + +
336A PRO* 5.7 1.7 - - - +
339A ILE* 3.4 33.4 - - + +
340A ARG* 3.7 0.2 - - - -
341A SER* 2.9 49.9 + - - +
343A PHE* 4.7 2.0 - + + -
417A VAL* 4.2 18.2 - - + +
418A LEU* 4.3 10.8 - - + -
421A ARG* 3.5 51.1 - - + +
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Residues in contact with LYS 332 (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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299A TRP 4.1 6.1 - - - +
300A MET 4.4 8.0 + - - +
301A MET 4.0 18.6 + - - +
302A ASP* 4.2 14.4 + - - +
303A PRO* 3.7 22.6 - - + +
330A HIS* 3.8 17.6 + - + +
331A TYR* 1.3 81.0 - - - +
333A THR* 1.3 72.7 + - - +
339A ILE 3.1 4.5 - - - +
340A ARG* 3.6 32.8 - - - +
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Residues in contact with THR 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A TYR* 3.3 35.7 + - + +
332A LYS* 1.3 82.5 - - - +
334A ASP* 1.3 62.9 + - - +
335A ALA* 4.1 9.2 - - + +
336A PRO* 4.5 11.7 - - + +
337A LEU 2.9 10.2 + - - +
338A ASN* 3.4 0.9 - - - -
339A ILE* 2.9 51.2 + - - +
340A ARG* 4.0 2.6 + - - +
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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