Contacts of the strand formed by residues 30 - 35 (chain B) in PDB entry 1H1B
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 MET 30 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TRP* 2.9 18.6 + - + +
28B PRO 3.3 2.8 - - - +
29B PHE* 1.3 83.0 - - + +
31B VAL* 1.3 82.7 + - - +
43B GLY* 4.2 4.7 - - - -
44B ALA 3.9 1.8 - - - +
45B THR* 5.2 0.2 - - - +
67B VAL 4.6 0.5 - - - +
69B GLY 4.4 13.5 + - - -
70B ALA 5.1 3.2 + - - +
139B MET* 3.9 18.2 - - - +
140B GLY* 4.1 11.9 - - - -
141B TRP* 3.7 30.5 - - + +
155B LEU* 3.9 23.1 - - + -
197B SER* 3.8 25.1 - - - +
198B PRO* 3.5 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PHE 3.5 13.0 - - - +
30B MET* 1.3 87.7 - - - +
32B SER* 1.3 66.9 + - - +
33B LEU* 4.2 0.4 - - + -
43B GLY* 3.2 6.8 - - - -
44B ALA* 2.8 51.3 + - + +
45B THR 4.2 0.4 - - - -
46B LEU* 3.7 18.8 - - + +
52B VAL* 4.3 2.9 - - + -
66B VAL* 3.5 30.3 - - + -
67B VAL 3.4 13.2 - - - +
68B LEU* 3.7 20.9 - - + -
141B TRP* 3.9 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 1.3 71.5 - - - +
33B LEU* 1.3 62.0 + - - +
34B GLN* 3.0 25.6 + - - +
40B HIS* 3.0 20.1 + - - -
42B CYS 3.9 2.9 - - - -
65B ARG 3.6 1.2 - - - +
67B VAL* 2.9 45.1 + - - +
70B ALA* 5.1 0.2 - - - -
73B LEU* 3.8 10.3 - - - +
141B TRP* 3.6 22.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 4.2 0.4 - - + -
32B SER* 1.3 73.0 - - - +
34B GLN* 1.3 57.3 + - - +
40B HIS* 3.6 3.1 - - - -
41B PHE* 3.0 48.6 + - + -
42B CYS* 2.8 27.3 + - + +
43B GLY 3.7 4.9 - - - +
44B ALA* 4.0 20.6 - - + -
52B VAL* 5.1 0.7 - - + -
54B SER* 3.7 27.6 - - - +
58B CYS* 5.0 4.0 - - + -
59B VAL* 5.1 4.7 - - + -
65B ARG* 3.5 9.2 - - + +
66B VAL* 3.9 37.9 - - + -
106B LEU* 4.6 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B SER* 3.0 21.0 + - - +
33B LEU* 1.3 77.6 - - - +
35B LEU* 1.3 62.5 + - - +
36B ARG 4.6 4.9 + - - +
38B GLY* 3.8 22.8 + - - -
39B GLY 3.3 14.4 - - - +
40B HIS* 4.2 7.2 - - - -
41B PHE* 3.5 5.6 - - - -
64B ALA 4.0 0.5 - - - +
65B ARG* 2.9 47.9 + - - +
67B VAL* 3.7 29.6 - - + +
73B LEU* 3.7 18.4 - - - +
80B ARG* 5.2 7.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN* 1.3 74.9 - - - +
36B ARG* 1.3 98.6 + - - +
39B GLY* 3.1 15.2 + - - +
41B PHE* 3.7 15.2 - - + -
62B ASN* 3.9 38.6 - - + +
64B ALA* 3.5 43.5 - - + +
65B VAL* 3.5 20.4 - - + +
----------------------------------------------------------
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