Contacts of the strand formed by residues 129 - 139 (chain A) in PDB entry 3CL0
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 CYS 129 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 4.0 10.5 - - + +
122A ILE* 4.5 1.6 - - + -
123A SER 3.7 3.6 - - - -
124A CYS* 2.1 46.2 - - - -
128A GLU* 1.3 77.6 - - - +
130A ARG* 1.3 64.2 + - - +
162A PRO* 4.1 3.5 - - - +
163A VAL* 3.4 42.0 + - + +
412A GLN* 3.5 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 3.4 4.2 - - - +
123A SER 2.9 32.3 + - - +
128A GLU* 3.1 47.6 + - + +
129A CYS* 1.3 73.0 - - - +
131A THR* 1.3 61.1 + - - +
132A PHE* 3.8 18.2 - - + -
160A SER* 2.9 49.2 + - - -
161A CYS* 3.5 15.7 - - - +
162A PRO* 4.4 14.6 - - - +
163A VAL* 3.6 5.2 - - - -
170A ASN 5.1 1.2 + - - -
172A ARG* 3.5 40.5 - - - +
189A TRP* 3.8 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASP* 5.6 1.6 - - - +
120A PRO* 4.4 12.8 - - + -
121A PHE 3.4 10.1 - - - +
122A ILE* 3.9 10.2 - - + +
130A ARG* 1.3 73.4 - - - +
132A PHE* 1.3 73.8 + - - +
133A PHE* 3.8 11.0 - - + -
160A SER* 3.1 5.0 - - - -
161A CYS* 2.9 43.8 + - - -
163A VAL* 3.4 25.3 - - - +
164A GLY 4.1 4.2 + - - -
165A GLU 5.9 1.1 - - - -
167A PRO* 6.6 0.2 - - + -
443A SER* 4.6 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PRO* 3.2 3.0 - - - +
121A PHE* 2.7 70.4 + + + +
123A SER* 4.0 8.3 - - - -
130A ARG* 3.8 22.4 - - + -
131A THR* 1.3 78.3 - - - +
133A PHE* 1.3 63.2 + - - +
158A LEU* 3.9 9.6 - - + -
159A MET 3.3 5.4 - - - -
160A SER* 3.7 20.2 - - - -
172A ARG* 5.8 0.2 - - - -
174A GLU* 3.9 25.4 - - + -
182A ALA* 3.7 18.6 - - + -
189A TRP* 3.6 46.0 - + - -
191A THR* 4.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE* 4.1 6.5 - + - -
117A ILE* 3.5 41.1 - - + -
119A GLU 4.1 7.6 - - - -
120A PRO* 4.2 3.6 - - + -
131A THR* 3.8 12.6 - - + -
132A PHE* 1.3 80.2 - - - +
134A LEU* 1.3 61.6 + - - +
135A THR* 3.5 21.8 - - + -
157A THR 3.5 0.3 - - - +
158A LEU* 3.4 9.6 - - - +
159A MET* 3.0 52.3 + - + -
160A SER* 3.8 6.1 - - - -
161A CYS* 3.7 18.8 - - - -
167A PRO* 3.5 26.9 - - + -
171A SER* 3.3 23.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 3.2 3.5 - - - -
118A ARG 3.0 35.0 + - - +
119A GLU* 3.7 24.7 + - + +
121A PHE* 6.4 0.7 - - + -
133A PHE* 1.3 72.3 - - - +
135A THR* 1.3 64.5 + - - +
136A GLN* 4.9 0.3 - - - +
156A ARG* 3.7 16.8 + - - +
157A THR 3.5 1.1 - - - -
158A LEU* 4.1 14.8 - - + -
177A ALA* 3.6 24.5 - - + +
178A TRP 3.5 26.7 - - - +
179A SER 4.0 0.4 - - - +
180A ALA* 3.9 25.1 - - + -
227A GLU* 3.9 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE* 3.9 18.0 - - + -
116A VAL 3.3 10.5 - - - -
117A ILE* 4.2 0.9 - - - -
133A PHE* 3.5 31.4 - - + -
134A LEU* 1.3 78.0 - - - +
136A GLN* 1.3 60.3 + - - +
137A GLY* 3.1 15.6 + - - -
156A ARG* 3.1 25.6 - - - -
157A THR* 2.7 33.0 + - - +
159A MET* 3.9 18.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 2.9 29.1 + - + +
117A ILE* 4.9 3.1 - - - +
118A ARG* 5.6 5.5 - - - +
134A LEU 4.9 1.6 - - - +
135A THR* 1.3 73.4 - - - +
137A GLY* 1.3 63.2 + - - +
138A ALA* 3.3 6.2 + - + +
144A HIS 5.1 1.2 - - - +
148A THR* 2.9 57.1 + - + +
150A LYS 3.3 8.7 + - - +
153A SER* 4.4 7.1 + - - -
155A HIS* 4.2 16.3 - - - +
156A ARG* 2.9 48.8 + - - +
439A THR 5.2 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE* 5.0 7.4 - - - -
135A THR* 3.1 16.2 + - - -
136A GLN* 1.3 79.6 - - - +
138A ALA* 1.3 58.8 + - - +
144A HIS* 5.0 3.8 - - - +
155A HIS* 4.0 16.0 + - - +
157A THR* 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE* 3.5 10.4 - - - -
116A VAL* 2.8 29.7 + - + +
136A GLN* 3.9 10.8 - - + +
137A GLY* 1.3 79.0 - - - +
139A LEU* 1.3 65.9 + - - +
144A HIS* 3.4 42.6 - - + +
145A SER* 4.0 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASP* 3.7 36.3 - - + +
114A VAL 3.3 16.8 - - - +
115A PHE* 4.0 11.7 - - + +
116A VAL* 3.5 7.9 - - - +
138A ALA* 1.3 80.5 - - - +
140A LEU* 1.3 70.3 + - - +
142A ASP* 3.5 28.7 + - + +
145A SER* 3.7 6.4 - - - -
169A PRO* 3.8 31.4 - - + +
----------------------------------------------------------
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