Contacts of the strand formed by residues 170 - 176 (chain H) in PDB entry 1U3H
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 170 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H PHE 3.9 0.3 - - - +
133H ARG* 3.5 1.8 - - - -
134H ASN* 2.8 44.8 + - - +
135H GLY 4.7 0.3 + - - -
168H GLY 3.9 10.3 - - - +
169H GLU* 1.3 78.4 - - - +
171H TYR* 1.3 73.0 + - - +
172H THR* 4.0 11.9 + - - +
187H GLU* 4.2 14.1 - - + +
188H TRP 4.0 3.8 - - - +
189H ARG* 2.9 49.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 171 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H ILE* 4.6 0.2 - - - +
115H LEU* 3.6 18.8 - - + -
131H TRP* 4.1 6.7 - - + -
132H PHE 3.3 9.6 - - - +
133H ARG* 4.0 23.8 + - + -
138H GLU* 5.1 1.6 - - - -
161H LEU* 3.6 24.0 - - + -
163H MET* 3.7 39.5 - - + +
164H THR 3.6 12.3 + - - -
165H PRO* 4.7 3.4 - - + -
169H GLU* 2.9 46.0 + - + -
170H VAL* 1.3 73.2 - - - +
172H THR* 1.3 63.8 + - - +
187H GLU* 3.3 4.5 - - - +
188H TRP* 2.8 56.3 + + + +
190H ALA* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 172 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H ARG 3.7 0.5 - - - +
131H TRP* 3.4 11.3 - - - -
132H PHE* 2.8 54.9 + - + +
135H GLY 5.7 1.9 + - - -
170H VAL* 4.0 9.5 + - - +
171H TYR* 1.3 79.9 + - - +
173H CYS* 1.3 71.7 + - - +
174H HIS* 3.9 2.5 + - + +
185H THR* 4.1 18.4 - - + -
186H VAL 3.2 12.8 - - - +
187H GLU* 4.0 16.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 173 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H VAL* 4.1 4.8 - - + +
101H ILE* 3.9 17.8 - - + +
117H CYS* 2.0 51.8 - - + -
129H VAL* 3.8 18.8 - - - -
130H ARG 3.5 4.9 - - - -
131H TRP* 4.4 5.8 - - + -
172H THR* 1.3 73.2 - - - +
174H HIS* 1.3 60.1 + - - +
175H VAL* 4.1 9.5 - - - +
184H ILE 3.5 1.7 - - - +
185H THR* 3.2 6.6 - - - -
186H VAL* 2.8 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 174 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H LYS* 3.7 1.9 - - + +
129H VAL* 3.4 5.4 - - - -
130H ARG* 2.9 62.4 + - + +
132H PHE* 3.6 28.2 - + + -
172H THR* 3.9 2.5 + - + +
173H CYS* 1.3 71.7 - - - +
175H VAL* 1.3 63.8 + - - +
176H GLU* 3.0 25.9 + - + -
183H PRO* 3.3 26.9 - - + +
184H ILE 3.5 2.0 - - - -
185H THR* 3.5 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H PRO* 4.2 13.5 - - + -
99H VAL* 3.9 18.2 - - + -
119H VAL* 3.8 30.7 - - + -
127H ILE* 3.8 27.8 - - + -
128H LYS 3.5 3.8 - - - +
129H VAL* 4.2 4.7 - - + -
173H CYS* 4.1 13.5 - - - +
174H HIS* 1.3 80.5 - - - +
176H GLU* 1.3 67.9 + - - +
180H LEU* 3.7 7.2 - - + +
183H PRO* 3.3 5.0 - - - +
184H ILE* 2.9 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H ILE* 3.5 5.2 - - - +
128H LYS* 3.0 67.0 + - + +
130H ARG* 3.4 8.7 + - - -
174H HIS* 3.0 25.7 + - + +
175H VAL* 1.3 75.7 - - - +
177H HIS* 1.3 63.2 + - - +
180H LEU* 4.7 1.3 - - - -
183H PRO* 3.9 22.8 - - + +
----------------------------------------------------------
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