Contacts of the strand formed by residues 137 - 146 (chain B) in PDB entry 2C10
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 ASN 137 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PHE* 2.8 32.8 + - - +
133B GLN* 3.4 9.4 - - - +
135B GLN 3.6 3.9 + - - +
136B PRO* 1.3 75.3 - - - +
138B VAL* 1.3 62.1 + - - +
139B SER* 2.8 17.0 + - - -
163B PRO* 4.5 13.9 - - + -
164B LEU 3.7 14.1 - - - +
165B PRO* 5.6 0.2 - - + -
166B TYR* 3.5 11.7 - - - -
1H NAG 1.5 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 3.8 15.9 - - + -
128B VAL 3.4 8.1 - - - +
129B PHE* 3.8 10.5 - - + -
137B ASN* 1.3 80.4 - - - +
139B SER* 1.3 62.8 + - - +
156B THR* 4.2 2.3 - - - +
164B LEU* 3.2 47.0 + - + +
165B PRO 3.9 13.2 - - - +
166B TYR* 4.2 5.2 - - + -
168B ARG* 5.5 0.2 - - + -
169B ARG* 4.1 23.8 - - + +
648B PHE* 3.5 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ALA 3.5 1.2 - - - +
127B ILE* 3.5 6.1 - - - +
128B VAL* 2.9 32.6 + - - +
130B PHE* 3.8 22.3 - - - -
137B ASN* 2.8 20.7 + - - -
138B VAL* 1.3 74.1 + - - +
140B GLU* 1.3 62.5 + - - +
141B LEU* 4.2 9.8 - - - +
154B ASP* 4.0 12.6 + - - -
156B THR* 3.4 12.2 + - - +
1H NAG 3.7 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 4.0 17.5 - - + +
126B ALA 3.6 3.6 - - - -
127B ILE* 4.3 17.0 - - + +
139B SER* 1.3 74.4 - - - +
141B LEU* 1.3 60.1 + - - +
154B ASP* 3.4 6.2 - - - +
155B VAL* 3.1 33.5 + - + -
156B THR* 3.0 10.6 + - - +
159B ARG* 3.0 25.3 + - - +
160B HIS* 2.5 40.1 + - - -
164B LEU* 3.4 14.8 - - + +
648B PHE* 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 4.6 3.1 - - + -
79B LEU* 4.0 12.6 - - + -
125B LEU* 3.5 3.6 - - - +
126B ALA* 2.8 47.8 + - + +
128B VAL* 3.8 25.6 - - + -
130B PHE* 4.9 4.3 - - + -
139B SER* 4.2 11.2 - - - -
140B GLU* 1.3 83.9 - - - +
142B VAL* 1.3 64.1 + - - +
143B VAL* 3.5 4.2 + - + +
152B MET* 3.8 37.0 - - + -
153B ARG 3.5 2.9 - - - +
154B ASP* 3.7 31.9 - - + +
2H NAG 4.6 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLN* 4.3 15.3 - - + +
123B GLU* 3.4 45.5 - - + +
124B ALA 3.1 5.4 - - - +
125B LEU* 3.9 19.5 - - + -
141B LEU* 1.3 70.1 - - - +
143B VAL* 1.3 61.5 + - - +
144B GLY 4.2 0.2 + - - -
151B TYR* 4.0 5.3 - - + +
152B MET* 3.3 3.3 - - - -
153B ARG* 2.9 42.8 + - + +
155B VAL* 4.0 22.9 - - + -
159B ARG* 4.4 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 3.9 28.9 - - + +
74B PHE* 3.7 21.3 - - + -
75B LEU* 3.8 27.1 - - + -
122B ARG 4.4 0.2 - - - +
123B GLU* 3.4 4.3 - - - -
124B ALA* 2.8 37.5 + - + +
126B ALA* 4.7 3.8 - - + +
141B LEU 4.0 11.0 - - - +
142B VAL* 1.3 77.2 - - - +
144B GLY* 1.3 61.3 + - - +
146B LEU* 4.9 2.5 - - - +
149B PRO* 3.8 15.3 - - + -
151B TYR* 3.5 12.6 - - - +
152B MET* 4.6 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG 4.3 2.0 - - - -
123B GLU* 4.7 0.7 - - - -
143B VAL* 1.3 77.9 - - - +
145B PRO* 1.3 71.4 - - - +
146B LEU* 5.5 0.4 - - - -
149B PRO* 3.8 1.3 - - - -
150B SER 2.7 26.0 + - - -
151B TYR* 2.8 39.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ALA* 4.3 13.0 - - + -
122B ARG 3.4 9.2 - - - +
144B GLY* 1.3 83.9 - - - +
146B LEU* 1.3 68.4 + - - +
148B HIS 3.1 15.4 - - - +
149B PRO* 3.0 27.0 - - - +
150B SER* 3.7 14.1 - - - +
151B TYR* 3.6 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 3.7 28.3 - - + -
67B GLU* 3.6 45.3 - - + +
70B ALA* 4.6 1.1 - - + -
71B VAL* 3.9 16.8 - - + -
122B ARG* 2.9 50.0 + - + +
123B GLU 4.1 10.8 - - - -
124B ALA 4.2 3.4 - - - +
143B VAL 4.9 2.5 - - - +
144B GLY* 5.5 0.2 - - - -
145B PRO* 1.3 83.5 - - - +
147B PRO* 1.3 74.1 - - + +
148B HIS 3.5 0.4 - - - -
149B PRO* 4.4 9.2 - - + -
----------------------------------------------------------
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