Contacts of the strand formed by residues 118 - 124 (chain H) in PDB entry 1W4R
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 THR 118 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H ARG 4.2 8.3 + - - -
20H GLN* 3.6 29.4 + - + +
22H GLN* 4.1 11.7 - - - +
43H PHE* 4.2 23.0 - - + -
92H ALA 3.0 12.7 + - - -
93H VAL* 3.3 11.5 - - + +
94H ILE* 2.8 26.7 + - - +
116H GLY 4.0 0.7 + - - -
117H LYS* 1.3 71.9 - - - +
119H VAL* 1.3 61.6 + - - +
120H ILE* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 119 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H GLN 2.9 13.9 + - - +
21H ILE* 3.3 8.0 - - + +
22H GLN* 2.8 27.4 + - - +
94H ILE* 3.3 15.5 - - + +
96H ILE* 4.2 9.6 - - + -
108H PHE* 4.9 1.1 - - + -
109H CYS* 3.7 40.6 - - + +
112H MET* 3.7 29.8 - - + -
113H ALA 4.0 4.7 - - - +
117H LYS* 4.1 6.5 - - + +
118H THR* 1.3 76.5 - - - +
120H ILE* 1.3 65.2 + - - +
121H VAL* 4.1 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H GLN* 3.5 24.0 - - + +
24H ILE* 3.8 20.6 - - + -
36H LEU* 3.3 21.2 - - + +
39H ARG* 3.8 31.9 - - + -
40H VAL* 4.3 13.2 - - + -
43H PHE* 4.3 13.0 - - + -
93H VAL* 4.4 4.5 - - + -
94H ILE 2.8 10.4 + - - +
95H GLY* 3.2 3.5 - - - -
96H ILE* 2.8 25.8 + - - +
118H THR* 4.0 21.3 - - + +
119H VAL* 1.3 79.6 - - - +
121H VAL* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 121 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H ILE* 4.7 3.1 - - + -
22H GLN 2.9 16.1 + - - +
23H VAL* 3.5 4.9 - - + +
24H ILE* 2.7 37.9 + - - +
96H ILE* 3.4 13.0 - - + +
99H GLY* 4.1 3.1 - - - -
105H ILE* 4.1 11.4 - - + -
109H CYS* 3.8 28.3 - - - -
119H VAL* 4.1 8.7 - - + -
120H ILE* 1.3 78.7 - - - +
122H ALA* 1.3 65.9 + - - +
123H ALA* 4.4 0.7 - - + -
136H ILE* 4.1 25.4 - - + -
139H LEU* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H ILE* 3.4 9.2 - - + -
32H LYS* 3.8 32.5 - - + +
36H LEU* 4.2 12.6 - - + +
96H ILE 2.9 9.6 + - - +
97H ASP* 3.8 18.8 - - - +
98H GLU 3.1 7.4 + - - -
99H GLY* 2.9 22.7 + - - -
120H ILE 4.2 0.4 + - - -
121H VAL* 1.3 71.6 - - - +
123H ALA* 1.3 61.8 + - - +
300H TTP 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H VAL* 5.5 0.4 - - + -
24H ILE 2.9 7.1 + - - -
25H LEU* 3.2 27.5 - - + +
32H LYS* 3.3 14.5 - - - +
99H GLY* 3.9 0.9 - - - +
100H GLN* 3.2 17.0 - - - +
121H VAL* 4.4 1.8 - - + -
122H ALA* 1.3 76.8 - - - +
124H LEU* 1.3 65.0 + - - +
136H ILE* 3.5 39.7 - - + -
300H TTP 4.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H GLY 3.3 17.9 - - - +
27H PRO* 3.4 3.6 - - + -
28H MET* 3.4 26.2 - - + +
32H LYS* 3.6 2.4 - - - +
100H GLN* 3.0 19.3 + - - +
123H ALA* 1.3 74.6 - - - +
125H ASP* 1.3 63.7 + - - +
126H GLY 3.9 11.2 - - - +
133H PHE* 3.7 26.9 - - + +
136H ILE* 3.6 16.6 - - - +
163H THR* 4.3 2.9 - - - +
300H TTP 3.5 65.1 - - + +
----------------------------------------------------------
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