Contacts of the strand formed by residues 165 - 173 (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 GLU 165 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A ARG* 2.8 29.9 + - - -
483A GLN* 3.3 13.8 + - - -
161B PRO* 5.9 0.9 - - - +
162B TYR* 3.3 31.1 + - - +
163B PRO 3.2 4.0 - - - +
164B GLY* 1.3 77.4 - - - +
166B ASP* 1.3 58.9 + - - +
167B ASN* 3.0 28.7 + - - +
513B ALA* 4.8 2.9 - - - -
514B GLU 3.1 12.3 - - - +
515B ARG* 2.6 41.1 + - - +
516B PHE* 3.9 6.7 - - - -
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Residues in contact with ASP 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ARG* 4.4 12.5 + - - -
165B GLU* 1.3 73.7 - - - +
167B ASN* 1.3 72.8 + - - +
168B GLU* 3.9 22.6 - - - +
512B VAL 3.7 1.4 - - - +
513B ALA* 3.2 4.9 - - - -
514B GLU* 2.9 36.7 + - + +
516B PHE* 3.4 23.7 - - + -
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Residues in contact with ASN 167 (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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482A VAL* 3.4 34.8 - - + +
483A GLN* 2.9 26.5 + - - +
159B VAL* 3.5 22.6 - - + +
160B VAL 4.7 2.2 - - - +
161B PRO* 5.5 2.7 - - + -
162B TYR* 3.8 9.7 - - - +
165B GLU* 3.0 34.1 + - - +
166B ASP* 1.3 79.3 + - - +
168B GLU* 1.3 60.8 + - - +
169B SER* 4.2 0.4 - - - -
512B VAL 3.7 1.4 - - - +
513B ALA* 3.1 14.2 - - - +
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Residues in contact with GLU 168 (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* 2.8 34.3 + - - +
154B TYR* 2.7 40.0 + - - -
155B PRO* 3.7 26.7 - - + +
166B ASP* 3.9 15.0 - - - +
167B ASN* 1.3 75.4 - - - +
169B SER* 1.3 60.4 + - - +
170B PHE* 3.8 9.5 - - + -
511B ALA* 3.7 0.5 - - - -
512B VAL* 2.8 39.4 + - - +
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Residues in contact with SER 169 (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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482A VAL 4.9 0.7 + - - -
484A PRO* 3.4 15.1 - - - +
155B PRO* 3.7 9.7 - - - +
157B VAL* 3.4 47.2 + - - +
159B VAL* 3.7 15.0 - - - +
167B ASN 4.2 1.4 + - - -
168B GLU* 1.3 72.0 + - - +
170B PHE* 1.3 63.9 + - - +
509B MET* 4.1 5.8 - - - -
510B LYS 3.2 6.5 - - - -
511B ALA* 3.3 24.8 - - - +
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Residues in contact with PHE 170 (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* 3.8 27.8 - - + -
462A ARG* 5.7 0.9 - - - -
1520A ACT 4.2 6.1 - - + -
154B TYR* 3.8 38.4 - + + -
155B PRO* 3.9 8.7 - - + -
156B ALA 4.4 3.4 - - - +
157B VAL* 4.0 6.3 - - - +
168B GLU* 3.8 22.4 - - + -
169B SER* 1.3 78.9 - - - +
171B TYR* 1.3 66.2 + - - +
172B VAL* 3.9 25.4 - - + -
509B MET* 3.4 5.3 - - - -
510B LYS* 2.9 51.5 + - + +
512B VAL* 3.7 21.1 - - + -
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Residues in contact with TYR 171 (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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501A ASP* 2.6 28.9 + - - -
152B TYR* 3.8 36.0 + + - +
154B TYR* 6.0 2.0 + - - +
156B ALA* 4.0 5.4 - - + +
157B VAL* 3.6 24.1 - - + +
170B PHE* 1.3 78.7 - - - +
172B VAL* 1.3 67.3 - - - +
173B PRO* 4.8 0.3 - - - +
504B ARG* 3.3 34.7 + - - -
507B LEU* 3.9 27.5 - - + +
508B GLU 3.3 12.1 - - - +
509B MET* 3.8 14.8 - - + +
2534B MPD 3.7 30.9 + - + +
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Residues in contact with VAL 172 (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* 5.2 2.2 - - + -
488A PHE* 4.5 12.3 - - + -
1520A ACT 3.8 31.4 - - + +
170B PHE* 3.9 16.2 - - + +
171B TYR* 1.3 80.6 - - - +
173B PRO* 1.3 75.2 - - + +
507B LEU* 3.4 7.2 - - - -
508B GLU* 2.8 59.1 + - + +
510B LYS* 5.2 3.1 - - + +
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Residues in contact with PRO 173 (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* 5.9 0.7 - - - -
87B PHE* 3.6 17.1 - - + -
91B LYS* 3.7 22.4 - - + +
98B ARG* 5.6 1.3 - - - +
171B TYR 4.8 0.7 - - - +
172B VAL* 1.3 96.7 - - + +
174B LEU* 1.3 63.0 + - - +
200B VAL 3.5 16.6 - - - +
201B GLY* 3.3 39.0 - - - +
202B ASN* 3.6 7.9 - - - +
506B PHE 3.7 9.2 - - - +
507B LEU* 3.8 2.9 - - + -
508B GLU* 4.0 7.4 - - - +
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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