Contacts of the strand formed by residues 157 - 161 (chain A) in PDB entry 1T9A
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 157 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PHE* 5.2 0.2 - - - -
146A ALA* 3.7 32.5 - - - -
149A TYR* 4.1 10.1 - - - -
150A ALA* 3.8 1.6 - - - +
155A LYS 3.6 2.0 + - - -
156A PRO* 1.3 71.7 - - - +
158A VAL* 1.3 61.2 + - - +
183A PRO 3.1 12.2 + - - -
184A MET* 3.2 7.7 - - - +
185A VAL 2.9 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 5.1 1.1 - - + -
102A MET* 4.4 8.1 - - - -
107A VAL* 3.8 21.5 - - + -
109A THR 4.0 14.6 + - - +
110A VAL* 3.6 17.0 - - + -
111A PHE* 2.8 33.0 + - - -
146A ALA* 4.3 1.6 - - - +
149A TYR* 5.5 0.2 - - - -
156A PRO 3.7 10.3 + - - +
157A GLY* 1.3 76.4 - - - +
159A VAL* 1.3 64.9 + - - +
160A LEU* 5.7 0.2 - - + -
185A VAL* 3.5 4.0 - - + +
187A PHE* 3.9 29.6 - - + -
234A PHE* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PHE 3.0 9.2 - - - +
142A ALA* 4.1 14.8 - - + +
143A GLY* 4.1 8.5 - - - +
146A ALA* 3.6 25.4 - - + -
158A VAL* 1.3 78.1 - - - +
160A LEU* 1.3 64.4 + - - +
161A VAL* 3.8 22.7 - - + -
170A VAL* 4.4 10.5 - - + -
184A MET* 4.3 13.9 - - + -
185A VAL 3.0 9.5 + - - +
186A VAL* 4.3 20.0 - - + -
187A PHE* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 4.3 15.0 - - + -
110A VAL* 3.9 16.8 - - + -
111A PHE 2.9 8.6 + - - +
112A GLY* 3.1 10.4 - - - -
113A TYR 3.2 0.3 + - - -
118A ILE* 3.7 26.7 - - + -
121A VAL* 3.9 19.3 - - + -
122A TYR* 2.7 55.5 + - + +
125A ILE* 3.8 23.1 - - + -
133A PHE* 4.5 2.9 - - + -
159A VAL* 1.3 73.4 - - - +
161A VAL* 1.3 58.9 + - - +
187A PHE* 3.4 21.5 - - + +
249A LEU* 5.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLY* 4.6 2.0 - - - -
113A TYR 3.6 14.8 - - - +
118A ILE* 3.7 12.0 - - - +
139A GLU* 3.4 31.6 - - + -
142A ALA* 4.9 0.9 - - + -
159A VAL* 3.8 19.7 - - + -
160A LEU* 1.3 79.1 - - - +
162A THR* 1.3 62.8 + - - +
166A GLY 3.5 20.2 - - - +
167A ALA* 4.2 0.4 - - - -
170A VAL* 4.1 8.5 - - + -
186A VAL* 4.9 0.2 - - + -
187A PHE 3.0 11.4 + - - +
188A THR* 3.6 26.9 - - + -
189A GLY 2.9 20.3 + - - -
----------------------------------------------------------
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