Contacts of the helix formed by residues 434 - 445 (chain B) in PDB entry 4Z4Q
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 GLY 434 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118A TYR* 5.4 8.1 - - - -
432B VAL 2.9 6.9 + - - +
433B GLU* 1.3 75.2 - - - +
435B ASP* 1.3 61.5 + - - -
436B SER* 3.3 2.9 - - - -
437B ALA 4.1 0.9 - - - -
438B GLY* 2.9 25.3 + - - -
454B PRO* 3.8 9.6 - - - +
455B LEU 3.2 17.7 + - - -
456B ARG* 4.9 2.7 - - - -
457B GLY 5.2 1.8 - - - -
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Residues in contact with ASP 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118A TYR* 5.7 0.6 + - - -
434B GLY* 1.3 72.0 - - - -
436B SER* 1.3 58.6 + - - +
438B GLY* 3.1 1.0 + - - -
439B GLY* 2.8 27.2 + - - -
454B PRO* 4.0 19.6 - - - +
455B LEU 5.0 0.2 + - - -
456B ARG* 3.2 41.1 + - - +
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Residues in contact with SER 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104A ASN* 3.0 28.8 + - - +
1114A ALA* 3.4 32.3 - - - +
1115A ALA 3.9 1.0 + - - -
1118A TYR* 3.4 39.4 + - - -
434B GLY* 3.3 1.0 - - - -
435B ASP* 1.3 78.2 - - - +
437B ALA* 1.3 60.8 + - - +
439B GLY 3.2 2.4 + - - -
440B SER* 3.3 7.0 + - - -
584B GLY* 6.1 2.7 - - - -
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Residues in contact with ALA 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118A TYR* 5.8 1.0 - - - -
432B VAL* 3.5 19.7 - - + +
433B GLU 3.7 13.4 + - - +
434B GLY* 3.6 2.6 + - - -
436B SER* 1.3 73.9 - - - +
438B GLY* 1.3 66.1 + - - +
439B GLY 3.1 0.4 - - - -
440B SER* 3.4 9.3 + - - +
441B ALA* 2.9 24.8 + - - +
504B MET* 5.4 0.2 - - + -
506B ASP* 5.6 0.2 - - - +
583B LEU* 4.0 33.4 - - + +
584B GLY* 5.4 2.8 - - - +
591B LEU* 4.6 3.3 - - + +
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Residues in contact with GLY 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B VAL* 3.5 10.2 - - - +
434B GLY 2.9 16.9 + - - -
435B ASP 3.1 4.2 + - - -
437B ALA* 1.3 75.5 - - - +
439B GLY* 1.3 51.3 + - - +
441B ALA* 3.2 2.1 + - - +
442B LYS* 2.7 35.6 + - - +
452B ILE* 3.9 10.1 - - - +
454B PRO* 4.0 20.2 - - - -
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Residues in contact with GLY 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104A ASN* 3.4 17.9 - - - -
1111A ASP* 5.4 5.8 - - - +
1112A PRO 5.8 0.2 - - - -
435B ASP 2.8 13.6 + - - -
436B SER 3.6 0.2 - - - -
437B ALA 3.1 0.4 - - - -
438B GLY* 1.3 73.4 - - - +
440B SER* 1.3 62.6 + - - +
442B LYS* 3.0 19.0 + - - +
443B GLN* 3.1 20.7 + - - +
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Residues in contact with SER 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103A GLY 4.7 0.2 - - - -
1104A ASN* 3.4 29.9 + - - +
436B SER 3.3 8.1 + - - -
437B ALA* 3.4 10.5 + - - -
439B GLY* 1.3 73.2 - - - +
441B ALA* 1.3 56.9 + - - +
443B GLN* 3.2 12.8 + - - -
444B GLY* 2.8 24.3 + - - -
583B LEU 5.2 4.0 + - - -
586B MET 3.9 13.5 + - - -
588B ALA* 3.4 17.1 + - - +
591B LEU* 3.9 16.4 - - - +
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Residues in contact with ALA 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B VAL* 4.3 0.7 - - + -
437B ALA 2.9 17.9 + - - +
438B GLY 3.6 3.6 - - - +
440B SER* 1.3 72.9 - - - +
442B LYS* 1.3 67.1 + - - +
443B GLN 3.1 1.3 - - - -
445B ARG* 2.9 28.8 + - - +
452B ILE* 3.8 24.4 - - + +
504B MET* 4.1 17.7 - - + -
591B LEU* 3.8 7.4 - - + +
596B MET* 4.0 15.7 - - - +
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Residues in contact with LYS 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109A ASP* 6.1 1.1 - - - +
1111A ASP* 4.9 11.2 - - - +
417B THR* 4.3 26.7 - - + +
438B GLY 2.7 18.3 + - - +
439B GLY* 3.0 12.5 + - - +
441B ALA* 1.3 71.8 - - - +
443B GLN* 1.3 59.6 + - + +
445B ARG* 2.8 35.6 + - - +
452B ILE* 4.0 8.2 - - + +
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Residues in contact with GLN 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104A ASN* 3.6 23.6 + - - +
1105A ASN* 5.7 0.2 - - - +
1106A GLY 3.9 16.8 + - - +
1107A SER* 4.2 13.9 - - - -
1111A ASP* 3.3 29.6 + - - +
1292A ASP* 5.0 1.2 - - - -
1293A ARG* 4.1 20.3 + - - +
439B GLY 3.1 21.1 + - - +
440B SER* 3.5 8.3 + - - +
441B ALA 3.1 0.6 - - - -
442B LYS* 1.3 80.1 - - + +
444B GLY* 1.3 59.7 + - - +
445B ARG* 3.8 2.1 + - - +
588B ALA* 3.7 18.9 + - + +
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Residues in contact with GLY 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1293A ARG* 3.0 15.7 + - - -
440B SER 2.8 14.8 + - - -
441B ALA* 3.3 2.2 + - - -
443B GLN* 1.3 75.0 - - - +
445B ARG* 1.3 68.6 + - - +
588B ALA* 3.6 23.3 - - - +
591B LEU* 5.5 0.4 - - - -
592B TRP* 3.3 20.7 - - - +
596B MET* 4.5 6.5 - - - -
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Residues in contact with ARG 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1292A ASP* 5.5 2.6 - - - +
1293A ARG* 2.9 15.8 + - - -
417B THR* 3.5 25.9 + - - +
418B PRO 3.2 25.5 + - - -
419B ALA* 3.7 7.5 - - - +
441B ALA 2.9 11.1 + - - +
442B LYS* 2.8 40.6 + - - +
443B GLN 3.5 1.8 - - - +
444B GLY* 1.3 81.6 - - - +
446B ASP* 1.3 59.8 + - - +
447B ARG* 3.5 48.0 + - + +
450B GLN* 3.0 44.8 + - + +
452B ILE* 4.1 8.4 - - + +
592B TRP* 4.2 1.8 - - - -
596B MET* 4.2 11.8 - - + -
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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