Contacts of the strand formed by residues 95 - 101 (chain A) in PDB entry 2HEI
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 ALA 95 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 6.0 0.4 - - + -
22A LYS 3.2 4.6 + - - +
23A LEU* 3.2 21.3 - - + -
24A VAL 3.0 19.9 + - - -
71A PHE* 5.0 0.9 - - + -
93A ALA* 3.6 4.0 - - - +
94A GLN* 1.3 82.0 - - - +
96A ALA* 1.3 63.2 + - - +
126A ILE* 3.7 8.2 - - - +
127A VAL* 3.2 13.5 - - + +
177A ILE* 3.7 27.1 - - + -
181A LEU* 4.6 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.5 1.1 - - - -
24A VAL* 3.1 18.2 - - + +
26A LEU* 4.9 2.0 - - + -
95A ALA* 1.3 76.8 - - - +
97A ILE* 1.3 60.4 + - - +
98A VAL 4.1 0.2 - - - -
118A LEU* 3.7 39.3 - - + -
126A ILE* 4.0 7.4 - - + -
127A VAL 2.9 8.5 + - - +
128A ILE* 3.4 4.0 - - + +
129A ALA* 2.8 31.4 + - - +
177A ILE* 5.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.0 10.8 - - + -
24A VAL 2.9 6.1 + - - -
25A LEU* 3.3 16.4 - - + +
26A LEU* 2.8 32.4 + - - +
36A LEU* 5.6 2.0 - - + -
96A ALA* 1.3 73.5 - - - +
98A VAL* 1.3 57.7 + - - +
99A VAL* 3.9 11.3 - - + +
129A ALA* 3.3 9.0 - - + +
131A ALA* 3.9 28.5 - - + +
173A LEU* 4.2 12.8 - - + -
174A PHE* 3.7 37.0 - - + -
177A ILE* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.5 17.0 - - + +
27A GLY* 4.7 0.9 - - - +
97A ILE* 1.3 72.1 - - - +
99A VAL* 1.3 63.2 + - - +
111A ALA* 3.6 41.1 - - + +
114A TRP* 3.9 9.6 - - + -
115A VAL* 4.0 21.1 - - + +
118A LEU* 3.6 31.0 - - + -
128A ILE* 4.4 2.0 - - + -
129A ALA 2.8 14.5 + - - +
130A LEU* 3.3 11.6 - - + +
131A ALA 2.9 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.2 6.7 - - + -
26A LEU 2.8 17.1 + - - +
27A GLY* 3.4 19.2 - - - -
28A GLU 4.2 0.9 + - - -
31A VAL* 3.7 26.4 - - + +
33A LYS* 4.0 12.6 - - + +
36A LEU* 3.8 29.6 - - + -
97A ILE* 3.9 20.9 - - + +
98A VAL* 1.3 81.0 - - - +
100A TYR* 1.3 75.3 + - - +
107A THR 4.7 0.9 - - - +
111A ALA* 4.5 2.3 - - - +
131A ALA* 3.4 9.0 - - + +
133A ASN* 3.8 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 3.9 9.9 - - - -
99A VAL* 1.3 74.2 - - - +
101A ASP* 1.3 70.5 + - - +
102A ILE* 3.9 12.0 - - + +
107A THR* 3.4 28.3 - - - +
108A PHE* 3.8 28.9 - + + +
111A ALA* 4.2 2.7 - - + -
130A LEU* 3.9 28.5 - - + -
131A ALA 2.9 13.8 + - - +
132A GLY* 3.3 26.2 - - - -
133A ASN* 2.9 30.5 + - - +
143A VAL* 3.6 25.6 - - + +
145A TYR* 5.8 0.2 - - - -
148A ALA* 3.2 21.5 - - + +
159A PHE* 3.4 12.0 - + - -
161A GLU* 4.4 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 4.7 1.4 - - - +
31A VAL* 4.0 19.1 - - + -
100A TYR* 1.3 77.4 - - - +
102A ILE* 1.3 64.4 + - - +
103A THR* 2.7 36.8 + - - +
104A ASN* 3.0 34.7 + - + +
107A THR* 3.0 14.1 + - + +
133A ASN 3.6 4.5 - - - -
134A LYS* 3.7 33.4 + - - +
143A VAL* 4.1 0.3 - - - +
----------------------------------------------------------
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