Contacts of the strand formed by residues 507 - 511 (chain A) in PDB entry 2EIE
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 VAL 507 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A VAL* 3.9 14.6 - - + -
447A LEU* 3.9 27.8 - - + -
453A PHE* 3.8 34.1 - - + -
499A SER* 4.4 9.9 - - - +
500A LEU 3.7 10.8 - - - +
501A LEU* 4.8 0.7 - - + -
502A LEU* 4.4 3.1 - - - -
506A ARG* 1.3 77.6 - - - +
508A PHE* 1.3 69.7 + - - +
509A ASN* 3.8 2.8 + - + +
526A GLN 3.6 1.4 - - - +
527A ILE* 3.4 6.9 - - - +
528A PHE* 2.9 47.5 + - + +
530A PRO* 4.7 2.5 - - + -
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Residues in contact with PHE 508 (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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165A ILE* 4.4 10.3 - - + -
167A LEU* 4.8 2.0 - - + -
171A PRO* 5.5 0.7 - - + -
183A VAL* 3.8 24.9 - - + -
185A MET* 3.8 28.9 - - + -
207A TRP* 3.5 35.4 - + + -
498A ILE* 3.9 20.4 - - + -
499A SER* 3.1 4.7 - - - -
500A LEU* 2.9 40.5 + - + +
502A LEU* 3.9 15.2 - - + +
507A VAL* 1.3 70.5 - - - +
509A ASN* 1.3 60.7 + - - +
510A GLY* 5.3 0.2 - - - -
525A ALA* 3.5 29.6 - - + -
526A GLN 3.8 2.2 - - - -
527A ILE* 3.7 18.2 - - + -
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Residues in contact with ASN 509 (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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161A TRP* 3.6 28.8 - - + -
443A THR* 3.7 7.3 + - - -
455A THR* 3.7 15.7 + - + +
489A ASN* 4.9 1.9 + - - -
493A ARG* 3.4 35.9 + - - +
497A SER* 5.0 0.2 - - - -
498A ILE 3.0 23.5 + - - +
499A SER* 3.0 16.7 + - - +
507A VAL* 3.8 5.1 + - + -
508A PHE* 1.3 74.5 - - - +
510A GLY* 1.3 58.8 + - - +
525A ALA* 3.2 3.5 - - - -
526A GLN* 2.7 41.9 + - - +
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Residues in contact with GLY 510 (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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171A PRO* 4.2 4.5 - - - -
493A ARG* 3.7 10.1 - - - -
497A SER* 3.2 7.3 - - - -
498A ILE* 2.8 45.2 + - - +
509A ASN* 1.3 75.1 - - - +
511A GLY* 1.3 63.6 + - - -
524A ASP 3.5 11.7 - - - -
525A ALA* 3.7 6.3 - - - +
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Residues in contact with GLY 511 (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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170A VAL* 4.2 1.3 - - - -
171A PRO* 3.5 27.9 - - - +
492A VAL 4.5 0.2 - - - +
493A ARG* 2.9 25.3 + - - -
496A HIS 3.9 5.6 - - - -
497A SER* 4.0 1.3 - - - -
510A GLY* 1.3 75.1 - - - -
512A GLY* 1.3 63.5 + - - -
522A HIS* 3.5 12.1 + - - +
524A ASP 3.1 13.3 + - - -
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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