Contacts of the strand formed by residues 122 - 127 (chain A) in PDB entry 1HTI
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 GLY 122 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR 2.9 12.9 + - - -
90A TRP* 3.4 21.2 - - - -
91A VAL 3.0 21.5 + - - -
120A GLY 4.2 0.2 + - - -
121A LEU* 1.3 75.4 - - - +
123A VAL* 1.3 65.7 + - - +
159A LYS* 3.1 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TRP* 3.5 3.6 - - - -
91A VAL* 3.4 9.6 - - + +
93A LEU* 3.7 23.8 - - + -
113A VAL* 4.1 15.3 - - + +
116A ALA* 3.5 30.1 - - + -
117A LEU* 3.9 21.8 - - + +
121A LEU 4.4 0.4 - - - +
122A GLY* 1.3 80.3 - - - +
124A ILE* 1.3 71.4 + - - +
125A ALA* 4.3 4.0 - - + +
159A LYS 2.8 12.0 + - - +
160A VAL* 3.2 10.1 - - + +
161A VAL 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 3.9 27.8 - - + -
9A GLY* 5.7 1.6 - - - -
40A VAL* 4.9 10.8 - - + -
62A ALA* 5.3 0.2 - - + -
90A TRP* 4.0 18.4 - - + -
91A VAL 2.9 8.1 + - - +
92A VAL* 3.6 25.4 - - + -
93A LEU 3.0 25.1 + - - +
123A VAL* 1.3 71.8 - - - +
125A ALA* 1.3 56.4 + - - +
126A CYS* 3.9 1.8 + - - -
161A VAL* 3.3 22.4 - - + -
163A ALA* 4.0 14.4 - - + -
207A ILE* 3.8 15.7 - - + -
230A LEU* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU 3.5 6.3 - - - +
109A ILE* 6.0 0.9 - - + -
113A VAL* 4.6 10.5 - - + -
123A VAL* 3.6 3.9 + - + -
124A ILE* 1.3 72.8 - - - +
126A CYS* 1.3 61.2 + - - +
127A ILE* 4.6 0.6 - - - +
150A ILE* 3.7 38.1 - - + -
160A VAL* 4.5 7.6 - - + -
161A VAL 2.8 11.1 + - - +
162A LEU* 3.6 11.9 - - + +
163A ALA 3.1 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 4.1 2.5 - - - -
93A LEU 3.0 16.9 + - - -
94A GLY* 3.0 22.3 - - - +
95A HIS* 3.8 19.3 - - - -
99A ARG* 2.8 31.9 + - - -
124A ILE 4.1 6.3 - - - -
125A ALA* 1.3 72.4 - - - +
127A ILE* 1.3 58.9 + - - +
150A ILE* 5.2 0.4 - - - +
163A ALA* 3.6 10.3 - - - +
165A GLU* 3.6 17.0 - - + +
230A LEU* 3.9 28.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 4.1 6.1 - - - +
125A ALA 4.9 1.6 - - - +
126A CYS* 1.3 80.3 - - - +
128A GLY* 1.4 57.5 + - - +
143A VAL* 4.4 11.7 - - + +
146A GLN* 3.6 34.8 - - + +
147A THR* 4.0 22.7 - - - +
150A ILE* 4.9 5.2 - - + -
162A LEU* 3.7 28.7 - - + -
163A ALA 3.1 20.2 + - - +
164A TYR* 3.6 5.1 - - + -
165A GLU* 3.0 28.4 + - - +
167A VAL* 5.1 0.2 - - - -
188A LEU* 3.9 28.5 - - + -
----------------------------------------------------------
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