Contacts of the strand formed by residues 52 - 57 (chain B) in PDB entry 2EHQ
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 ARG 52 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS* 4.0 26.0 + - + +
50B LYS 5.1 2.8 + - - +
51B GLU* 1.3 78.8 + - - +
53B MET* 1.3 65.1 + - - +
54B VAL* 4.5 12.5 - - + +
67B THR* 3.9 33.0 + - - +
68B THR 3.2 13.0 - - - +
70B LYS* 4.2 11.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG* 1.3 77.2 - - - +
54B VAL* 1.3 64.3 + - - +
67B THR* 3.1 8.3 - - - -
68B THR* 2.8 38.3 + - - +
69B ALA 3.4 14.8 - - - +
70B LYS* 3.9 11.9 - - + -
210B GLU* 3.7 31.0 - - + +
213B VAL* 4.4 13.6 - - + +
237B PRO* 3.5 13.7 - - - +
238B GLY* 3.2 48.5 - - - -
239B VAL* 4.3 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG* 4.5 13.7 - - + +
53B MET* 1.3 79.2 - - - +
55B SER* 1.3 63.6 + - - +
56B LEU* 4.0 16.2 + - + +
64B VAL* 3.8 34.3 - - + -
66B GLY 3.9 2.7 - - - +
67B THR* 4.2 11.2 - - + -
210B GLU 4.8 6.2 - - - +
213B VAL* 5.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B MET 4.2 0.4 + - - -
54B VAL* 1.3 73.5 - - - +
56B LEU* 1.3 55.6 + - - +
64B VAL* 3.5 6.1 - - - +
65B VAL* 2.8 36.4 + - - +
66B GLY 2.9 16.9 + - - +
123B GLU* 2.6 32.0 + - - +
210B GLU 4.9 2.0 - - - -
211B ASP* 3.7 4.2 + - - +
213B VAL* 4.1 10.3 - - - -
214B VAL* 3.9 8.1 - - - -
2540B NA 3.2 16.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 4.0 15.7 + - + +
55B SER* 1.3 75.9 + - - +
57B ASN* 1.3 60.5 + - - +
58B PRO* 3.3 6.6 - - + +
61B PRO* 3.5 39.3 - - + +
62B SER 5.4 0.2 - - - -
63B GLU 3.7 3.1 - - - +
64B VAL* 4.0 26.2 - - + -
65B VAL* 4.1 5.5 - - - +
123B GLU 3.5 1.7 - - - +
364B VAL 5.6 0.2 - - - +
397B TYR* 4.8 7.2 - - + +
2540B NA 2.5 28.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 1.3 71.1 - - - +
58B PRO* 1.4 62.4 - - - +
59B SER* 2.8 23.7 + - - -
60B ALA* 2.8 47.3 + - - +
61B PRO* 2.9 4.6 - - - +
63B GLU* 2.8 41.7 + - - +
65B VAL* 3.6 12.8 - - + +
121B VAL 5.0 0.5 - - - +
122B TYR* 3.3 38.9 - - - +
355B GLU* 5.2 3.2 + - - -
2535B MPD 6.0 1.2 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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