Contacts of the strand formed by residues 123 - 130 (chain B) in PDB entry 2C11
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 GLU 123 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 4.2 2.4 - - - +
101B LEU* 3.6 8.9 - - - +
102B GLN* 3.1 38.8 + - + +
103B LEU 5.3 1.9 - - - +
104B PRO* 5.8 1.0 - - - +
105B PRO* 5.5 6.8 - - - +
121B ALA* 3.1 19.2 + - - +
122B ARG* 1.3 75.9 - - - +
124B ALA* 1.3 61.6 + - - +
142B VAL* 3.7 19.1 - - + +
143B VAL 3.3 10.3 - - - +
146B LEU* 4.8 2.0 - - - -
151B TYR* 3.0 36.3 + - + +
153B ARG* 3.5 23.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 3.4 29.8 - - + -
71B VAL* 4.0 24.0 - - + -
99B VAL* 4.1 7.9 - - + -
100B GLU 3.3 4.9 - - - +
102B GLN* 3.7 4.5 - - - -
123B GLU* 1.3 75.5 - - - +
125B LEU* 1.3 61.4 + - - +
141B LEU 3.5 1.4 - - - +
142B VAL* 3.3 5.8 - - - -
143B VAL* 2.9 33.5 + - - +
146B LEU* 4.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B SER* 3.7 2.6 + - - +
99B VAL* 3.2 3.3 + - - -
100B GLU* 3.0 34.9 + - + +
101B LEU 5.0 1.8 - - - +
102B GLN* 3.6 21.1 - - + +
124B ALA* 1.3 73.0 - - - +
126B ALA* 1.3 62.8 + - - +
127B ILE* 4.2 6.5 - - + +
140B GLU* 3.9 26.9 - - + +
141B LEU 3.5 21.5 - - - +
142B VAL* 4.0 12.8 - - + -
159B ARG* 3.1 32.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 5.1 0.2 - - + -
75B LEU* 4.0 19.3 - - + -
96B VAL* 4.4 3.4 - - + -
98B SER 2.8 13.0 - - - +
99B VAL* 3.4 19.5 - - + -
124B ALA 4.0 0.2 + - - -
125B LEU* 1.3 74.3 - - - +
127B ILE* 1.3 63.0 + - - +
128B VAL* 3.9 4.5 + - + +
139B SER 3.4 2.3 - - - +
140B GLU* 3.7 1.4 - - - -
141B LEU* 3.0 39.9 + - + +
143B VAL* 5.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 3.6 2.9 - - - +
97B PHE* 2.8 36.6 + - + -
98B SER* 2.9 26.1 + - - +
125B LEU* 5.2 8.1 - - + +
126B ALA* 1.3 76.3 - - - +
128B VAL* 1.3 64.6 + - - +
129B PHE* 4.0 24.5 - - + -
138B VAL* 4.7 0.7 - - + -
139B SER 3.3 13.2 - - - +
140B GLU* 4.4 13.0 - - + +
344B PHE* 4.5 8.1 - - + -
647B VAL* 4.4 11.2 - - + -
648B PHE* 3.6 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 5.5 1.1 - - + -
79B LEU* 3.6 27.8 - - + -
83B LEU* 4.3 2.9 - - + -
95B CYS 3.3 22.0 - - - +
96B VAL* 4.0 6.5 - - + -
126B ALA* 4.1 12.1 - - + +
127B ILE* 1.3 80.1 - - - +
129B PHE* 1.3 65.5 + - - +
130B PHE* 3.7 25.0 + - + -
138B VAL* 3.3 4.2 - - - +
139B SER* 3.0 30.4 + - - +
141B LEU* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ASP 4.8 0.4 - - - +
94B ASN* 3.4 5.5 - - - -
95B CYS* 2.8 41.9 + - - +
97B PHE* 3.3 39.9 - + + -
127B ILE* 4.0 10.3 - - + -
128B VAL* 1.3 77.0 - - - +
130B PHE* 1.3 64.5 + - - +
131B GLY 3.7 0.4 - - - -
137B ASN 4.0 3.4 - - - -
138B VAL* 3.5 15.7 - - + -
166B TYR* 3.6 15.7 - - + +
169B ARG* 3.7 38.4 - - + -
170B PRO* 3.9 16.6 - - + -
172B LEU* 3.4 41.1 - - + -
648B PHE* 5.6 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 3.6 33.4 - - + -
83B LEU* 5.5 0.2 - - + -
94B ASN* 2.9 30.7 - - + +
128B VAL* 3.7 24.5 - - + -
129B PHE* 1.3 78.8 - - - +
131B GLY* 1.3 56.5 + - - +
132B ARG 3.4 0.4 - - - -
133B GLN* 3.2 21.5 - - - +
136B PRO* 3.0 27.2 - - - +
137B ASN* 2.7 29.3 + - - +
139B SER* 3.3 19.5 - - - -
141B LEU* 4.8 4.7 - - + -
166B TYR* 3.6 1.9 - - - -
1G NAG 3.5 39.9 - - - -
2G NAG 4.6 4.9 - - + -
----------------------------------------------------------
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