Contacts of the strand formed by residues 114 - 123 (chain A) in PDB entry 4PSQ
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 TYR 114 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TRP* 3.2 10.2 - - - -
108A ASP* 3.1 37.5 + - + -
109A THR* 2.7 43.5 + - - -
110A ASP* 3.1 39.4 + - + +
113A THR* 1.3 82.0 + - - +
115A ALA* 1.3 62.2 + - - +
116A VAL* 4.3 8.1 - - + -
137A PHE 3.4 7.2 - - - +
144A LEU* 3.7 18.6 - - + -
148A ALA* 3.8 18.4 - - + -
151A ILE* 3.3 38.9 - - + +
152A VAL* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 3.5 36.3 - - + -
24A TRP* 3.7 8.0 - - + -
106A ILE* 5.2 1.1 - - + -
108A ASP 3.5 7.4 - - - +
109A THR* 3.5 4.3 - - - +
114A TYR* 1.3 79.2 - - - +
116A VAL* 1.3 67.8 + - - +
135A PHE 3.9 0.3 - - - +
136A VAL* 3.6 4.3 - - - +
137A PHE* 2.8 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ILE* 3.7 3.3 - - - +
107A VAL* 2.8 42.6 + - + +
108A ASP 2.9 16.0 + - - +
114A TYR* 4.3 8.5 - - + -
115A ALA* 1.3 78.8 - - - +
117A GLN* 1.3 64.5 + - - +
134A SER* 4.1 9.4 - - - +
135A PHE 3.6 4.7 - - - +
136A VAL* 4.9 5.6 - - + -
152A VAL* 3.9 37.2 - - + +
155A ARG* 4.4 15.5 - - + -
156A GLN* 5.4 2.7 - - + -
159A LEU* 4.2 18.8 - - + -
165A TYR* 4.6 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A HIS* 3.7 39.0 + - + +
105A TRP 3.3 10.3 - - - +
106A ILE* 4.6 7.4 - - + +
107A VAL* 4.1 0.7 - - - -
115A ALA 4.1 0.8 - - - -
116A VAL* 1.3 75.9 - - - +
118A TYR* 1.3 84.8 + - - +
119A SER* 3.8 3.8 - - - -
133A TYR* 3.4 23.5 - - - +
134A SER* 2.6 34.3 + - - -
135A PHE* 2.9 44.2 + - - +
137A PHE* 3.9 22.7 - - + -
201A 2WL 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 3.9 2.6 - - + +
9A PHE* 3.7 27.9 - + - -
105A TRP* 2.9 57.4 + + + +
107A VAL* 3.3 20.0 - - + -
117A GLN* 1.3 84.1 + - - +
119A SER* 1.3 71.9 + - - +
120A CYS* 3.9 18.2 - - + -
129A CYS* 3.3 30.5 - - - +
132A SER* 3.9 20.4 - - - -
133A TYR 3.5 10.3 - - - -
134A SER* 4.4 1.3 - - - -
159A LEU* 4.0 29.7 + - + -
161A LEU* 4.0 19.5 - - + -
209A EDO 4.2 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASP* 3.8 8.5 - - - +
103A ASP* 2.7 31.4 + - - -
105A TRP* 5.8 0.2 - - - -
117A GLN* 3.8 2.2 - - - -
118A TYR* 1.3 81.9 - - - +
120A CYS* 1.3 63.6 + - - +
121A ARG* 4.0 0.9 + - - +
132A SER* 3.2 7.3 - - - -
133A TYR* 2.9 68.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 3.9 18.8 - - + -
103A ASP* 3.6 21.2 + - - +
105A TRP* 6.2 1.2 - - + -
118A TYR* 3.9 15.4 - - + +
119A SER* 1.3 73.8 + - - +
121A ARG* 1.3 59.8 - - - +
122A LEU 3.3 20.4 - - - -
123A LEU* 3.9 7.0 - - - -
129A CYS* 2.0 49.8 - - - -
204A EDO 3.5 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PRO* 3.4 27.5 - - - +
33A GLU 4.1 8.7 + - - -
36A PHE* 4.5 0.2 - - - -
90A TYR* 3.3 4.9 + - - -
102A ASP* 2.9 43.8 + - - +
119A SER* 4.0 3.8 + - - +
120A CYS* 1.3 75.5 - - - +
122A LEU* 1.3 65.9 + - + +
131A ASP* 2.8 34.1 + - - +
133A TYR* 3.5 21.8 - - + -
201A 2WL 2.8 41.0 + - - -
204A EDO 3.8 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 5.6 3.4 - - - +
120A CYS* 3.3 12.9 - - - -
121A ARG* 1.3 84.5 - - + +
123A LEU* 1.3 65.1 + - - +
130A ALA* 2.7 44.8 + - + -
131A ASP* 3.4 18.0 + - + +
204A EDO 4.6 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 3.5 27.6 - - + -
120A CYS* 3.9 7.2 - - - -
122A LEU* 1.3 84.9 - - - +
124A ASN* 1.3 71.2 + - - +
127A GLY* 3.4 28.5 - - - +
128A THR 3.5 3.1 - - - +
130A ALA* 4.2 3.2 - - - +
204A EDO 3.8 24.1 - - - -
----------------------------------------------------------
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