Contacts of the strand formed by residues 3 - 10 (chain X) in PDB entry 4LAH
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 3 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2X THR* 1.3 72.3 - - - +
4X SER* 1.3 59.0 + - - +
83X ILE* 3.8 15.7 - - + +
84X TYR* 4.0 21.5 - - + -
90X VAL* 3.4 31.9 - - + +
92X ILE* 4.0 13.2 - - + -
102X MET* 3.7 22.0 - - + -
105X LYS 4.0 17.7 - - - +
106X VAL* 3.5 11.6 - - + +
107X ASP* 2.8 47.3 + - - +
108X ASP* 3.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 4 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2X THR* 3.7 1.2 - - - +
3X LEU* 1.3 72.3 - - - +
5X ILE* 1.3 53.8 + - - +
89X HIS* 2.6 31.1 + - - -
90X VAL 2.8 7.5 + - - +
91X PHE* 3.3 20.2 - - - -
92X ILE* 2.7 36.7 + - - +
106X VAL* 4.0 5.6 - - - -
108X ASP* 2.6 28.9 + - - -
110X TYR* 3.9 8.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 5 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4X SER* 1.3 74.0 - - - +
6X LEU* 1.3 71.3 + - - +
7X VAL* 3.8 18.4 - - + -
91X PHE* 5.0 0.2 - - - -
92X ILE* 3.8 15.5 - - + -
99X PHE* 4.0 13.9 - - + +
102X MET* 4.3 1.3 - - + -
103X ILE* 3.8 32.8 - - + +
106X VAL* 3.7 22.9 - - + +
108X ASP 3.0 8.1 + - - -
109X MET* 3.9 16.8 - - + -
110X TYR* 2.8 36.2 + - - +
124X PHE* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 6 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4X SER 4.1 0.2 + - - -
5X ILE* 1.3 72.5 - - - +
7X VAL* 1.3 62.0 + - - +
31X HIS* 5.3 1.3 - - + +
32X VAL* 4.0 40.2 - - + +
35X LEU* 3.6 18.2 - - + -
36X SER* 4.5 2.7 - - - -
41X LEU* 4.4 4.0 - - + -
91X PHE* 4.0 30.7 - - + -
92X ILE 2.9 12.8 + - - +
93X PHE* 4.1 19.3 - - + -
99X PHE* 3.2 11.3 - - - -
110X TYR* 3.4 29.4 - - + +
201X 1VO 2.6 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 7 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5X ILE* 3.8 6.1 - - + -
6X LEU* 1.3 74.4 - - - +
8X ALA* 1.3 58.9 + - - +
9X HIS* 4.4 4.3 - - + +
15X ILE* 3.8 15.3 - - + -
99X PHE* 3.5 27.8 - - + -
110X TYR 3.1 8.0 + - - +
111X ILE* 3.3 29.9 - - + +
112X THR 2.8 31.0 + - - +
124X PHE* 3.7 32.5 - - + -
201X 1VO 3.3 14.2 + - - -
202X NAP 3.4 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 8 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7X VAL* 1.3 70.8 - - - +
9X HIS* 1.3 60.8 + - - +
15X ILE* 3.5 7.1 - - - +
21X LEU* 5.3 0.7 - - + -
23X TRP* 3.4 26.6 - - + +
28X ASP* 3.8 17.5 - - - +
112X THR* 3.2 11.4 - - - +
114X ILE* 4.4 2.7 - - + -
201X 1VO 3.3 17.4 + - + +
202X NAP 2.7 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 9 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7X VAL* 4.4 4.9 - - + -
8X ALA* 1.3 74.9 - - - +
10X ASP* 1.3 78.1 + - - +
11X LEU 5.9 0.2 - - - -
13X ARG* 3.8 23.4 - - + +
14X VAL 3.2 11.7 - - - +
15X ILE* 3.6 14.6 - - + -
23X TRP* 4.1 0.4 - - - -
111X ILE* 3.6 23.9 - - + +
112X THR 3.0 8.2 + - - +
113X VAL* 3.3 15.0 - - + -
114X ILE* 2.8 29.5 + - - -
124X PHE* 4.1 23.3 - + + -
127X TYR* 2.8 31.9 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 10 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9X HIS* 1.3 93.1 + - - +
11X LEU* 1.3 60.2 + - - +
12X GLN* 2.8 17.3 + - - +
13X ARG 3.0 10.0 + - - -
14X VAL* 2.9 43.8 + - - +
23X TRP* 4.0 15.1 - - + -
113X VAL* 4.8 2.2 - - - +
114X ILE* 3.1 16.8 - - + +
116X GLY 3.2 11.8 - - - +
117X LYS* 3.6 1.8 - - - -
118X PHE* 2.8 35.1 + - + +
----------------------------------------------------------
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