Contacts of the strand formed by residues 125 - 130 (chain A) in PDB entry 2H57
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 ILE 125 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE* 3.3 38.8 - - + +
92A PHE* 4.2 7.0 - - + -
109A LEU* 5.1 3.8 - - + -
112A LEU* 5.4 1.6 - - + -
113A LEU* 3.4 33.2 - - + -
123A ILE 3.8 8.5 - - - +
124A PRO* 1.3 75.5 - - - +
126A LEU* 1.3 61.3 + - - +
127A PHE* 3.5 32.8 + - + -
152A ILE* 4.7 10.8 - - + -
155A LYS* 4.1 15.0 - - + -
156A PRO 3.0 9.6 + - - +
157A TRP* 3.1 26.5 - - + +
158A HIS 3.2 5.2 + - - +
176A TRP* 3.7 3.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE 2.8 11.6 + - - +
91A ILE* 3.2 18.1 - - + +
92A PHE 2.8 26.0 + - - +
124A PRO 4.1 0.4 + - - -
125A ILE* 1.3 70.1 - - - +
127A PHE* 1.3 73.2 + - - +
128A PHE* 3.8 24.9 - - + -
158A HIS* 3.7 26.2 - - + +
160A CYS* 4.2 3.4 - - - -
173A GLY* 3.5 47.3 - - - +
174A VAL* 4.2 1.8 - - + +
176A TRP* 3.9 13.7 - - + -
177A LEU* 4.2 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.2 34.8 - + + -
94A ILE* 4.9 2.7 - - + -
109A LEU* 3.7 33.2 - - + -
125A ILE* 3.5 31.0 - - + -
126A LEU* 1.3 82.2 - - - +
128A PHE* 1.3 63.1 + - - +
129A ALA 4.1 0.2 - - - -
147A LEU* 4.7 7.6 - - + -
149A LEU* 3.7 35.9 - - + -
152A ILE* 4.0 14.4 - - + -
157A TRP* 4.2 8.3 - + + -
158A HIS 2.8 21.8 + - - +
159A ILE* 3.3 19.6 - - + -
160A CYS 3.0 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 3.8 33.4 - - + -
37A LEU* 6.0 2.0 - - + -
91A ILE* 3.7 28.5 - - + -
92A PHE 3.0 8.5 + - - +
93A VAL* 4.1 5.5 - - + +
94A ILE* 2.9 29.6 + - - +
126A LEU* 3.8 26.9 - - + -
127A PHE* 1.3 76.7 - - - +
129A ALA* 1.3 58.8 + - - +
130A ASN* 3.2 2.3 + - + -
159A ILE* 4.9 0.2 - - - -
160A CYS* 3.3 24.5 - - + -
162A SER* 3.7 23.1 - - - +
169A GLY 3.8 18.2 - - - -
170A LEU* 3.7 27.8 - - + -
173A GLY* 4.2 4.3 - - - -
174A VAL* 4.9 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE* 3.9 7.2 - - - -
96A SER* 3.0 23.2 + - - +
127A PHE 4.1 0.6 - - - -
128A PHE* 1.3 67.2 - - - +
130A ASN* 1.3 58.1 + - - +
132A MET* 4.2 3.3 + - - +
138A VAL 5.0 0.2 - - - +
140A SER* 3.8 30.7 - - - +
143A VAL* 3.9 14.6 - - + -
159A ILE* 4.2 5.5 - - + +
160A CYS 2.7 14.2 + - - +
161A ALA* 3.3 5.2 - - + +
162A SER 3.0 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER 2.9 23.3 + - - +
29A GLY* 3.6 6.7 - - - -
33A ILE* 3.9 7.5 - - + +
93A VAL* 3.8 11.4 - - + -
94A ILE 2.8 15.5 + - - +
96A SER* 2.8 31.5 + - - -
128A PHE 4.2 0.9 - - - +
129A ALA* 1.3 71.1 - - - +
131A LYS* 1.3 70.1 + - - +
132A MET 3.2 2.2 - - - -
162A SER* 2.6 34.0 + - - +
164A ALA* 3.3 19.7 + - - +
201A GTP 3.1 27.0 + - - -
----------------------------------------------------------
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