Contacts of the strand formed by residues 553 - 557 (chain E) in PDB entry 4WEB
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 553 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496E CYS* 4.5 4.9 - - - -
510E CYS* 3.7 1.0 - - - +
511E PHE* 3.2 24.7 + - - -
551E TRP* 3.3 2.5 - - - +
552E PHE* 1.3 81.1 - - - +
554E CYS* 1.3 70.7 + - - -
566E CYS 3.1 13.9 - - - -
567E GLY* 3.9 1.6 - - - -
603E SER 3.6 0.9 - - - -
604E GLY* 3.5 17.4 - - - +
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Residues in contact with CYS 554 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508E VAL* 4.2 1.3 - - + -
509E TYR 3.2 11.7 - - - +
510E CYS* 2.0 42.8 - - - +
511E PHE* 4.1 2.7 - - - -
541E LEU* 3.9 18.4 - - + -
551E TRP* 3.8 11.9 - - - -
553E GLY* 1.3 78.2 - - - -
555E THR* 1.3 69.4 + - - +
556E TRP* 3.9 12.3 - - + -
565E THR* 3.5 4.3 - - - -
566E CYS* 2.7 39.2 + - - +
604E GLY* 4.4 0.2 - - - -
605E PRO* 4.4 3.5 - - - +
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Residues in contact with THR 555 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508E VAL* 3.8 0.5 - - - -
509E TYR* 2.9 28.1 + - - -
511E PHE* 3.6 6.0 - - - -
554E CYS* 1.3 84.5 + - - +
556E TRP* 1.3 69.1 + - - +
563E THR* 3.6 26.2 - - + -
564E LYS 3.2 8.3 - - - +
565E THR* 3.7 2.1 - - + +
605E PRO* 3.5 14.4 - - - +
615E TYR* 4.0 6.3 - - - -
621E HIS* 3.3 25.0 - - - +
622E TYR* 3.2 27.6 + - + +
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Residues in contact with TRP 556 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496E CYS 5.1 2.7 - - - -
499E VAL* 3.8 28.7 - - + +
504E VAL* 3.5 25.6 - - + -
507E PRO 4.1 2.0 - - - +
508E VAL* 3.5 33.7 - - + -
541E LEU* 3.6 21.3 - - + -
554E CYS* 3.9 4.0 - - + -
555E THR* 1.3 84.0 - - - +
557E MET* 1.3 76.9 + - - +
558E ASN* 4.4 4.1 - - - +
563E THR* 3.5 8.5 - - - +
564E LYS* 2.7 57.0 + - + +
565E THR 3.8 7.0 - - - -
566E CYS* 3.6 35.7 - - + -
621E HIS* 3.7 18.8 + - - -
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Residues in contact with MET 557 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504E VAL* 3.3 4.3 - - - +
505E CYS* 2.5 55.0 + - + +
507E PRO 5.0 0.6 + - - -
556E TRP* 1.3 85.6 - - - +
558E ASN* 1.3 66.8 + - - +
561E GLY* 3.7 21.8 - - - +
562E TYR 3.6 7.4 - - - +
563E THR* 3.2 43.5 - - - +
620E TRP* 5.1 8.1 - - - +
621E HIS* 4.2 18.1 + - + +
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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