Contacts of the helix formed by residues 553 - 562 (chain A) in PDB entry 3WAJ
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 TYR 553 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ASN* 5.7 0.2 - - - -
503A TRP* 3.4 42.6 - + + -
549A SER* 3.5 20.6 - - - +
550A TRP* 3.8 22.2 - + + +
551A TRP 3.1 1.6 + - - -
552A ASP* 1.3 81.6 - - + +
554A GLY* 1.3 64.1 + - - +
555A HIS 3.3 2.9 - - - -
556A TRP* 3.2 35.3 + + + +
557A ILE* 3.1 26.8 + - + +
611A ASP* 2.8 24.2 + - - -
613A GLU* 2.9 6.6 + - - -
614A MET* 3.8 21.1 - - + -
618A LYS* 2.5 35.8 + - - +
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Residues in contact with GLY 554 (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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550A TRP 4.3 1.0 + - - -
551A TRP 3.3 7.9 + - - -
552A ASP 3.4 0.6 - - - -
553A TYR* 1.3 77.5 - - - +
555A HIS* 1.3 64.9 + - - +
557A ILE* 3.3 1.8 + - - -
558A GLU* 3.0 21.2 + - - +
565A PRO* 3.5 22.8 - - - +
567A ALA 3.3 24.1 + - - -
568A ASN* 4.5 1.3 - - - -
569A PRO* 3.9 5.8 - - - -
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Residues in contact with HIS 555 (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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46A ASN* 3.5 29.6 - - + +
47A ASP* 3.4 25.8 + - - -
49A TRP* 4.3 6.2 - - + -
50A TYR* 3.5 33.8 - + + +
553A TYR 3.3 1.2 - - - -
554A GLY* 1.3 75.5 - - - +
556A TRP* 1.3 58.6 + - - +
558A GLU* 3.5 5.8 + - - +
559A ALA* 2.8 33.3 + - - +
568A ASN* 4.2 6.5 + - - -
569A PRO* 3.4 33.3 - - + +
570A PHE* 3.5 40.0 - + - -
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Residues in contact with TRP 556 (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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45A GLY* 2.9 24.0 + - - -
46A ASN* 3.6 23.5 + - - -
49A TRP* 3.5 30.2 - + + +
498A GLY* 3.7 5.4 - - - -
499A PRO* 3.3 46.0 - - + +
500A ASN 4.9 0.4 - - - -
503A TRP* 3.9 27.4 - + + -
507A LEU* 3.7 14.5 - - + +
553A TYR* 3.2 45.4 + + - +
555A HIS* 1.3 73.0 - - - +
557A ILE* 1.3 59.3 + - - +
559A ALA* 4.5 0.9 - - - +
560A VAL* 2.7 45.0 + - + +
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Residues in contact with ILE 557 (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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503A TRP* 4.6 4.5 - - + -
507A LEU* 4.1 21.3 - - + -
510A MET* 5.0 0.9 - - - -
547A VAL* 4.0 32.5 - - + +
549A SER* 3.9 29.6 - - - +
550A TRP 5.7 0.2 - - - +
553A TYR* 3.1 21.5 + - + +
554A GLY* 3.7 6.7 - - - +
556A TRP* 1.3 74.1 - - - +
558A GLU* 1.3 59.3 + - - +
561A ALA* 3.0 35.5 + - + +
562A HIS 3.3 3.1 + - - -
563A ARG* 3.5 19.8 + - + +
565A PRO* 4.2 20.9 - - + -
609A VAL* 4.7 4.3 - - + -
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Residues in contact with GLU 558 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A TYR* 3.4 15.6 - - + -
53A ARG* 3.0 22.6 + - + -
69A ASP* 2.7 28.4 - - - +
71A PHE* 3.3 18.5 - - + +
72A THR* 3.4 26.1 + - - -
524A TYR* 3.4 19.8 - - + -
554A GLY 3.0 16.4 + - - +
555A HIS* 3.8 4.0 + - - +
557A ILE* 1.3 79.3 - - - +
559A ALA* 1.3 62.7 + - - +
562A HIS* 3.2 20.3 + - - -
563A ARG 3.5 12.3 - - - +
565A PRO* 4.2 4.9 - - + -
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Residues in contact with ALA 559 (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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49A TRP* 3.6 35.2 - - + +
52A TYR* 3.9 28.7 + - + -
53A ARG* 4.6 2.5 - - + -
511A ARG* 5.1 1.6 + - - -
524A TYR* 3.6 12.1 + - - +
555A HIS 2.8 22.1 + - - +
556A TRP 4.5 0.2 - - - +
558A GLU* 1.3 74.8 - - - +
560A VAL* 1.3 60.0 + - - +
562A HIS* 3.7 15.0 + - - -
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Residues in contact with VAL 560 (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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49A TRP* 3.5 35.2 - - + -
499A PRO* 5.8 1.1 - - + -
504A TYR* 3.9 23.6 - - + +
507A LEU* 3.6 23.3 - - + +
508A THR* 3.7 28.1 - - + +
511A ARG* 3.7 22.2 + - - +
556A TRP* 2.7 28.1 + - + +
559A ALA* 1.3 74.8 - - - +
561A ALA* 1.3 62.4 + - - +
562A HIS* 3.3 2.1 + - - -
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Residues in contact with ALA 561 (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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507A LEU* 3.4 33.2 - - + +
510A MET* 3.9 26.9 - - + -
511A ARG* 3.2 12.2 - - - +
556A TRP 3.6 0.4 + - - -
557A ILE* 3.0 17.1 + - - +
560A VAL* 1.3 78.9 - - - +
562A HIS* 1.3 66.8 + - - +
563A ARG* 3.1 20.7 + - + +
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Residues in contact with HIS 562 (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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52A TYR* 6.0 0.6 + - - -
56A GLU* 4.9 8.7 + - - -
71A PHE* 3.6 9.2 - - + -
511A ARG* 3.2 39.4 + - - -
520A TYR* 3.3 15.3 - - + +
521A ASP* 2.8 29.7 + - + +
524A TYR* 3.4 44.1 - + + -
557A ILE 3.3 0.2 + - - -
558A GLU 3.2 25.2 + - - -
559A ALA 3.7 12.8 + - - -
560A VAL 3.3 0.2 - - - -
561A ALA* 1.3 78.2 - - - +
563A ARG* 1.3 76.2 + - - +
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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