Contacts of the strand formed by residues 98 - 103 (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 ASN 98 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G SER* 6.4 0.7 - - - -
96G PRO* 5.2 3.3 - - - +
96H GLN 3.6 3.0 + - - +
97H PRO* 1.3 72.2 - - - +
99H VAL* 1.3 63.6 + - - +
100H VAL* 4.1 15.9 - - + +
118H SER 3.0 5.4 - - - +
119H VAL* 3.2 2.9 - - - -
120H THR* 2.7 54.0 + - - +
121H ASP* 4.1 12.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H PRO* 3.8 7.6 + - + +
98H ASN* 1.3 81.4 + - - +
100H VAL* 1.3 66.7 + - - +
117H CYS* 3.6 28.5 - - - -
118H SER 3.4 2.2 - - - +
119H VAL* 4.4 2.7 - - + -
173H CYS* 4.1 6.5 - - + +
175H VAL* 3.9 21.1 - - + -
184H ILE* 3.7 33.8 - - + +
186H VAL* 3.6 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 100 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G PRO* 3.4 43.5 - - + -
98G LEU* 5.5 13.2 - - + -
98H ASN* 4.1 15.7 - - - +
99H VAL* 1.3 81.5 - - - +
101H ILE* 1.3 70.7 + - - +
102H SER* 4.9 5.8 - - - +
116H VAL 3.5 1.0 - - - +
117H CYS* 3.6 1.6 - - - -
118H SER* 2.9 34.3 + - - +
186H VAL* 5.1 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H VAL* 1.3 80.9 - - - +
102H SER* 1.3 69.8 + - - +
115H LEU* 4.5 4.9 - - + -
116H VAL 3.4 5.2 - - - +
117H CYS* 4.5 2.5 - - - -
131H TRP* 4.0 27.1 - - + -
171H TYR 4.6 0.4 - - - +
173H CYS* 3.9 22.4 - - + +
186H VAL* 3.5 44.7 - - + +
187H GLU 4.1 0.9 - - - +
188H TRP* 3.7 46.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H VAL* 5.2 7.0 - - - -
101H ILE* 1.3 78.7 - - - +
103H LEU* 1.3 63.6 + - - +
104H SER* 5.2 1.2 + - - -
114H THR 3.8 0.2 - - - +
115H LEU* 3.4 4.0 - - - -
116H VAL* 2.7 50.2 + - - +
118H SER* 5.0 3.5 + - - -
188H TRP* 5.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G GLU 5.2 3.8 - - - +
102H SER* 1.3 80.0 - - - +
104H SER* 1.3 69.0 + - - +
105H ARG 3.6 12.1 + - - +
106H THR 4.4 17.5 - - - +
107H GLU* 3.7 26.5 - - + +
113H ASN* 3.9 22.4 - - + +
114H THR 3.6 7.2 - - - +
115H LEU* 3.4 25.6 - - + -
163H MET* 4.5 5.6 - - - -
165H PRO* 5.9 2.5 - - + -
188H TRP* 3.7 20.5 - - + +
----------------------------------------------------------
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