Contacts of the strand formed by residues 507 - 515 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B TYR* 3.7 40.2 - - + -
171B TYR* 3.9 28.5 - - + -
172B VAL* 3.4 24.0 - - - +
173B PRO* 3.8 4.5 - - + -
174B LEU* 3.9 3.1 - - - -
200B VAL* 3.8 32.1 - - + +
284B ARG* 2.8 27.0 + - - -
503B LEU 3.7 16.8 - - - +
504B ARG* 3.0 21.6 + - - +
505B LEU 3.4 0.6 - - - -
506B PHE* 1.3 82.3 - - - +
508B GLU* 1.3 59.8 + - - +
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Residues in contact with GLU 508 (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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465A HIS* 3.7 22.6 + - - -
488A PHE* 3.4 33.2 - - + +
489A LYS 5.2 0.2 + - - -
494A ASN* 3.4 21.2 - - - +
171B TYR* 3.3 8.1 - - - -
172B VAL* 2.8 47.6 + - + +
173B PRO 4.0 9.4 - - - +
174B LEU* 3.7 26.7 - - + +
254B ARG* 3.8 15.6 + - - -
284B ARG* 3.9 4.1 + - - +
504B ARG* 4.4 1.8 - - - +
507B LEU* 1.3 75.5 - - - +
509B MET* 1.3 60.2 + - - +
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Residues in contact with MET 509 (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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467A GLY 4.1 0.3 - - - +
484A PRO* 3.6 33.7 - - + -
488A PHE* 3.3 17.9 - - - -
494A ASN* 2.9 10.2 + - - +
496A LYS* 3.2 38.6 + - + -
499A ALA* 4.7 3.1 - - + -
501A ASP* 3.2 35.0 - - + +
157B VAL* 3.8 27.6 - - + -
169B SER* 4.1 3.6 - - - -
170B PHE 3.4 11.2 - - - +
171B TYR* 3.8 16.8 - - + +
504B ARG* 4.2 4.7 - - - +
508B GLU* 1.3 73.9 - - - +
510B LYS* 1.3 67.8 + - - +
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Residues in contact with LYS 510 (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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460A ALA 3.4 8.7 + - - -
461A ARG 2.8 23.1 + - - -
464A PHE 2.7 22.8 + - - +
466A VAL 3.4 22.0 - - - +
467A GLY 3.6 3.1 - - - +
469A LEU* 3.8 17.5 - - - -
488A PHE* 4.0 8.1 - - + -
496A LYS* 4.7 0.2 - - - -
1520A ACT 2.6 38.9 + - + +
168B GLU 3.9 1.4 - - - +
169B SER* 3.2 4.3 - - - -
170B PHE* 2.9 52.2 + - + -
172B VAL* 5.2 2.4 - - + +
508B GLU 4.3 0.4 + - - -
509B MET* 1.3 76.6 - - - +
511B ALA* 1.3 63.1 + - - +
512B VAL* 3.8 10.8 - - + -
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Residues in contact with ALA 511 (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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467A GLY 2.8 11.7 + - - +
468A ASN* 3.4 10.7 + - - +
469A LEU 2.9 26.0 + - - +
470A TYR* 5.8 0.7 - - - -
482A VAL 5.7 0.2 - - - +
483A GLN* 4.5 7.4 - - + -
484A PRO* 3.6 31.6 - - + +
496A LYS* 4.2 1.1 - - - +
168B GLU 3.7 0.4 - - - -
169B SER* 3.3 20.4 - - - +
510B LYS* 1.3 72.0 - - - +
512B VAL* 1.3 63.8 + - - +
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Residues in contact with VAL 512 (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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461A ARG* 3.4 40.3 + - + +
469A LEU* 3.3 13.2 - - + +
471A PHE* 3.8 25.1 - - + -
483A GLN* 6.2 0.2 - - - -
166B ASP* 3.7 1.4 - - - +
167B ASN* 3.7 1.8 - - - -
168B GLU* 2.8 41.4 + - - +
170B PHE* 3.7 24.5 - - + -
510B LYS* 3.8 25.1 - - + -
511B ALA* 1.3 78.0 - - - +
513B ALA* 1.3 62.3 + - - +
514B GLU 4.3 0.2 + - - -
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Residues in contact with ALA 513 (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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469A LEU 2.9 6.7 + - - -
470A TYR* 3.3 26.8 - - + -
471A PHE* 2.7 35.2 + - - +
473A ARG* 4.6 5.5 - - - +
483A GLN* 4.0 7.6 - - + +
165B GLU* 4.5 5.4 - - - +
166B ASP 3.2 5.8 - - - +
167B ASN* 3.1 23.3 - - - +
511B ALA 4.3 0.4 - - - -
512B VAL* 1.3 77.0 - - - +
514B GLU* 1.3 53.4 + - - +
515B ARG 4.2 0.4 - - - -
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Residues in contact with GLU 514 (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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454A ARG* 2.8 44.4 + - - -
457A LEU* 3.9 14.0 - - - +
458A GLU* 4.8 0.7 - - - +
461A ARG* 4.4 12.9 + - - +
471A PHE* 3.8 24.0 - - + +
472A ASN* 4.7 5.1 + - - +
165B GLU* 3.1 7.8 - - - -
166B ASP* 2.9 35.4 + - + +
512B VAL 4.3 0.2 + - - -
513B ALA* 1.3 74.3 - - - +
515B ARG* 1.3 67.3 + - - +
516B PHE* 3.4 36.2 + - + -
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Residues in contact with ARG 515 (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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471A PHE 3.1 7.5 + - - -
472A ASN* 3.8 37.5 + - - +
473A ARG* 3.5 37.9 - - + +
474A LYS* 5.3 7.5 - - - +
162B TYR* 4.3 15.5 + - - -
163B PRO 4.6 3.5 + - - -
164B GLY* 3.6 12.3 - - - -
165B GLU* 2.6 40.7 + - - +
513B ALA 4.2 0.4 - - - -
514B GLU* 1.3 76.1 - - - +
516B PHE* 1.3 68.8 + - - +
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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