Contacts of the strand formed by residues 507 - 515 (chain A) in PDB entry 2EIT
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 LEU 507 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A TYR* 3.7 39.5 - - + -
171A TYR* 3.9 24.5 - - + -
172A VAL* 3.3 24.7 - - - +
173A PRO* 3.8 3.4 - - + -
174A LEU* 3.9 2.9 - - - -
200A VAL* 3.7 27.8 - - + +
284A ARG* 2.8 22.6 + - - +
503A LEU 3.6 15.5 - - - +
504A ARG* 2.9 26.1 + - - +
505A LEU 3.4 0.4 + - - -
506A PHE* 1.3 87.0 - - - +
508A GLU* 1.3 60.8 + - - +
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Residues in contact with GLU 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A TYR* 3.3 7.1 - - - -
172A VAL* 2.8 53.0 + - + +
173A PRO 4.1 9.5 - - - +
174A LEU* 3.7 23.3 - - + +
254A ARG* 3.7 20.7 + - - -
284A ARG* 4.0 3.9 + - - +
504A ARG* 4.3 1.8 - - - +
507A LEU* 1.3 74.3 - - - +
509A MET* 1.3 60.8 + - - +
465B HIS* 3.8 23.2 + - - -
488B PHE* 3.4 26.8 - - + +
489B LYS 5.2 0.2 + - - -
494B ASN* 3.4 20.7 - - - +
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Residues in contact with MET 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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157A VAL* 3.9 27.1 - - + -
169A SER* 4.1 3.8 - - - -
170A PHE 3.4 10.5 - - - +
171A TYR* 3.9 15.0 - - + +
504A ARG* 4.1 5.8 - - - +
508A GLU* 1.3 74.3 - - - +
510A LYS* 1.3 67.7 + - - +
467B GLY 4.2 0.3 - - - +
484B PRO* 3.6 33.7 - - + -
488B PHE* 3.3 9.3 - - - -
494B ASN* 2.8 18.3 + - - +
496B LYS* 3.2 37.4 + - + -
499B ALA* 4.7 3.8 - - + -
501B ASP* 3.2 35.9 - - + +
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Residues in contact with LYS 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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168A GLU 3.9 1.1 - - - +
169A SER* 3.2 5.2 - - - -
170A PHE* 2.9 54.0 + - + -
172A VAL* 5.1 3.3 - - + +
508A GLU 4.2 0.2 + - - -
509A MET* 1.3 76.8 - - - +
511A ALA* 1.3 62.4 + - - +
512A VAL* 3.9 10.3 - - + -
460B ALA 3.4 8.3 + - - -
461B ARG 2.8 21.7 + - - -
464B PHE 2.7 17.7 + - - +
466B VAL 3.3 28.0 - - - +
467B GLY 3.6 3.4 - - - +
469B LEU* 3.8 16.8 - - - -
488B PHE* 4.0 7.9 - - + -
496B LYS* 4.7 0.2 - - - -
2520B ACT 2.6 40.2 + - + +
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Residues in contact with ALA 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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168A GLU 3.7 0.2 - - - -
169A SER* 3.3 20.6 - - - +
510A LYS* 1.3 72.5 - - - +
512A VAL* 1.3 62.3 + - - +
467B GLY 2.8 12.2 + - - +
468B ASN* 3.4 9.2 + - - +
469B LEU 2.8 26.9 + - - +
470B TYR* 5.8 0.5 - - - -
482B VAL 5.7 0.2 - - - +
483B GLN* 4.5 7.9 - - + -
484B PRO* 3.6 31.9 - - + +
496B LYS* 4.2 0.6 - - - +
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Residues in contact with VAL 512 (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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166A ASP* 3.7 2.9 - - - +
167A ASN* 4.6 0.9 - - - -
168A GLU* 2.8 37.1 + - - +
170A PHE* 3.8 24.2 - - + -
510A LYS* 3.9 24.7 - - + -
511A ALA* 1.3 77.5 - - - +
513A ALA* 1.3 60.3 + - - +
461B ARG* 3.4 37.5 + - + +
469B LEU* 3.3 12.8 - - + +
471B PHE* 3.7 27.8 - - + -
483B GLN* 6.1 0.4 - - - -
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Residues in contact with ALA 513 (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 GLU* 4.4 5.6 - - - +
166A ASP 3.2 6.3 - - - +
167A ASN* 3.2 23.1 - - - +
511A ALA 4.2 0.4 - - - -
512A VAL* 1.3 75.5 - - - +
514A GLU* 1.3 53.8 + - - +
515A ARG 4.1 0.4 - - - -
469B LEU 2.8 7.1 + - - +
470B TYR* 3.3 27.8 - - + +
471B PHE* 2.7 36.0 + - - +
473B ARG* 4.6 5.8 - - - +
483B GLN* 4.1 7.0 - - + +
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Residues in contact with GLU 514 (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 GLU* 3.2 7.2 - - - -
166A ASP* 2.9 34.1 + - + +
512A VAL 4.3 0.2 + - - -
513A ALA* 1.3 72.6 - - - +
515A ARG* 1.3 66.8 + - - +
516A PHE* 3.3 37.3 + - + -
454B ARG* 2.8 45.1 + - - -
457B LEU* 3.7 14.0 - - - +
458B GLU* 4.8 0.7 - - - +
461B ARG* 4.4 15.4 + - - +
471B PHE* 3.7 20.3 - - + +
472B ASN* 4.6 5.0 + - - +
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Residues in contact with ARG 515 (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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162A TYR* 4.3 16.4 + - - -
163A PRO 4.8 3.5 + - - -
164A GLY* 3.7 13.7 - - - -
165A GLU* 2.7 40.1 + - + +
513A ALA 4.1 0.6 - - - -
514A GLU* 1.3 75.8 - - - +
516A PHE* 1.3 66.4 + - - +
471B PHE 3.1 6.9 + - - -
472B ASN* 3.9 29.2 + - - +
473B ARG* 3.6 46.0 - - + +
474B LYS* 5.3 7.5 - - - +
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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