Contacts of the strand formed by residues 52 - 59 (chain A) in PDB entry 2P5V
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 52 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.9 24.5 - - + -
17A LEU* 5.4 1.6 - - + -
43A LEU* 4.4 7.2 - - + -
46A LEU* 3.2 17.0 + - + -
47A GLU* 3.7 30.7 - - + +
50A GLY* 4.1 2.4 - - - -
51A ILE* 1.3 74.0 - - - +
53A ARG* 1.3 61.2 + - - +
54A GLN 4.0 12.8 - - - +
55A TYR* 3.5 45.5 - - + +
57B ALA* 4.5 6.5 - - + -
58B LEU 3.7 5.6 - - - +
59B LEU* 3.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLY* 4.4 13.7 - - - +
51A ILE 3.6 1.2 + - - -
52A VAL* 1.3 74.4 - - - +
54A GLN* 1.3 76.0 + - - +
58B LEU* 2.9 53.8 + - - +
59B LEU 3.4 23.4 + - - -
60B SER* 4.1 7.8 - - - +
61B PRO* 5.0 4.2 - - - +
148B HIS* 3.5 41.9 + - - -
149B THR* 6.0 1.2 - - - +
150B THR* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 3.5 5.9 - - - +
53A ARG* 1.3 104.8 + - - +
55A TYR* 1.3 69.2 + - - +
56A ALA* 3.8 5.5 - - - +
18B GLN 3.1 26.9 + - - -
19B GLU* 3.2 29.7 + - - +
57B ALA* 3.6 2.6 - - - -
58B LEU* 2.7 46.2 + - + +
149B THR* 5.3 7.1 + - - -
150B THR* 4.9 3.2 + - - -
151B SER* 5.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.6 9.4 - - + -
21A GLY 3.7 13.7 - - - +
43A LEU* 3.2 20.8 - - - +
47A GLU* 2.4 34.8 + - + -
52A VAL* 3.5 17.0 - - + +
54A GLN* 1.3 76.4 + - - +
56A ALA* 1.3 58.8 + - - +
19B GLU 3.2 16.1 + - - +
20B ASN* 3.7 0.6 - - - -
21B GLY* 2.7 22.4 + - - +
22B ARG* 3.5 52.9 - - + +
56B ALA 3.5 3.8 - - - +
57B ALA* 3.7 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLN* 3.8 6.5 - - - +
55A TYR* 1.3 75.1 - - - +
57A ALA* 1.3 64.0 + - - +
58A LEU* 3.6 9.3 + - + +
17B LEU 3.8 0.9 - - - -
18B GLN 3.2 20.9 - - - +
21B GLY* 3.9 4.5 - - - -
55B TYR* 3.4 2.7 - - - -
56B ALA* 2.9 33.8 + - - +
58B LEU* 4.0 10.3 - - + -
150B THR* 3.7 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA* 1.3 73.3 - - - +
58A LEU* 1.3 64.2 + - - +
59A LEU* 4.3 13.2 - - + -
14B LEU* 6.5 0.2 - - + -
17B LEU* 2.8 41.0 + - + +
18B GLN* 3.5 23.7 - - - +
21B GLY* 3.8 2.6 - - - -
52B VAL* 4.5 5.8 - - + -
54B GLN 3.5 6.5 - - - +
55B TYR* 3.8 18.8 - - + -
150B THR* 5.0 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA* 4.0 13.5 - - + +
57A ALA* 1.3 79.4 - - - +
59A LEU* 1.3 65.5 + - - +
149A THR* 6.4 0.4 - - - -
150A THR* 3.9 30.1 - - + +
52B VAL* 3.7 0.5 - - - -
53B ARG* 3.0 52.0 + - - +
54B GLN* 2.7 35.4 + - + +
56B ALA* 4.0 12.3 - - + -
58B LEU* 5.1 2.0 - - + -
150B THR* 3.6 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 4.3 7.4 - - + +
58A LEU* 1.3 83.5 - - - +
60A SER* 1.3 65.5 + - - +
61A PRO* 3.5 6.8 - - - +
64A VAL* 4.7 1.8 - - + -
14B LEU* 4.2 17.5 - - + +
18B GLN* 3.4 39.9 + - + +
51B ILE* 3.1 20.2 - - + +
52B VAL* 3.9 21.3 - - + -
53B ARG* 3.3 17.6 + - - -
150B THR 5.5 1.4 + - - -
152B LEU* 3.9 20.2 - - + +
154B LEU* 4.1 28.0 - - + -
----------------------------------------------------------
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