Contacts of the strand formed by residues 133 - 141 (chain B) in PDB entry 1VGC
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 133 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ALA* 1.3 73.0 - - - +
134B THR* 1.3 64.3 + - - +
135B THR* 3.5 8.7 + - - -
161C PRO* 4.4 10.5 - - - +
162C LEU 3.0 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PHE* 4.9 5.1 - - + -
131B ALA* 2.7 36.1 + - - +
132B ALA 3.3 0.8 + - - -
133B GLY* 1.3 76.4 - - - +
135B THR* 1.3 66.7 + - - +
136B CYS* 3.7 17.7 + - - -
161C PRO* 3.3 1.8 - - - +
162C LEU* 3.0 36.2 + - + +
201C CYS* 4.8 6.5 - - + -
202C LYS 5.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLY 3.5 7.0 + - - -
134B THR* 1.3 77.2 - - - +
136B CYS* 1.3 66.7 + - - +
137B VAL* 6.1 0.2 - - + -
159C SER* 3.8 28.7 - - - +
160C LEU* 3.5 11.4 - - - +
161C PRO* 4.3 5.4 - - - +
201C CYS* 5.1 2.4 - - - +
202C LYS 5.5 1.6 + - - -
207C TRP* 5.8 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B THR* 3.8 8.7 - - - -
135B THR* 1.3 80.1 - - - +
137B VAL* 1.3 67.6 + - - +
159C SER* 3.1 7.3 - - - -
160C LEU* 2.9 33.2 + - - +
162C LEU* 3.8 21.3 - - + -
199C LEU* 4.0 14.4 - - + -
200C VAL 3.1 7.4 - - - +
201C CYS* 2.2 49.4 - - - +
207C TRP* 5.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.9 27.8 - - + -
27B TRP* 3.7 25.1 - - + -
136B CYS* 1.3 78.6 - - - +
138B THR* 1.3 71.1 + - - +
139B THR* 4.1 7.0 - - + -
157C GLN* 4.5 0.4 - - + -
158C ALA 3.3 14.6 - - - +
159C SER* 4.2 5.6 - - - +
160C LEU* 4.2 0.2 - - - -
198C PRO 4.0 0.2 - - - +
199C LEU* 3.4 5.0 - - - -
200C VAL* 2.8 52.2 + - + +
207C TRP* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 3.4 18.0 - - + +
137B VAL* 1.3 75.4 - - - +
139B THR* 1.3 64.3 + - - +
157C GLN* 3.5 1.4 - - - -
158C ALA* 2.9 42.5 + - + +
160C LEU* 4.0 21.3 - - + +
188C VAL* 6.2 0.2 - - + -
189C SER 6.0 0.4 - - - -
190C SER* 3.8 20.0 + - - +
194C ASP* 6.1 0.2 - - - +
198C PRO 2.9 18.2 + - - -
199C LEU* 4.4 7.4 - - - -
213C VAL* 3.8 18.2 - - - +
228C TYR* 4.1 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 3.7 6.2 - - - +
27B TRP* 3.5 48.1 - - + +
29B TRP* 5.3 0.3 + - - -
30B GLN* 2.8 28.8 + - - +
137B VAL* 4.1 5.2 - - + -
138B THR* 1.3 85.0 + - - +
140B GLY* 1.3 59.0 + - - +
155C LEU* 4.6 4.3 - - - -
156C GLN 3.4 14.4 - - - +
157C GLN* 3.8 4.5 - - + -
194C ASP* 4.3 6.6 - - - +
197C GLY* 4.7 4.3 - - - -
198C PRO* 3.3 26.1 + - - +
200C VAL* 6.0 1.6 - - + +
213C VAL* 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 3.9 2.2 - - - +
30B GLN* 4.1 9.9 - - - -
139B THR* 1.3 78.6 - - - +
141B TRP* 1.3 58.4 + - - -
142B GLY 3.4 0.6 + - - -
155C LEU* 3.7 14.0 - - - +
156C GLN* 3.1 36.5 + - - +
194C ASP* 3.3 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLN* 3.6 35.4 - - + -
31B VAL* 3.8 4.0 - - - -
32B SER* 3.7 22.0 - - - -
40B HIS* 3.8 37.1 + + + +
67B VAL 5.7 0.2 - - - -
70B GLU* 3.5 36.8 - - + -
71B PHE 3.0 24.0 + - - -
73B GLN* 3.5 21.8 - - + +
140B GLY* 1.3 71.8 - - - -
142B GLY* 1.3 65.1 + - - +
151C THR* 3.2 21.5 - - - +
152C PRO* 3.4 18.1 - - - +
153C ASP 3.2 17.9 + - - -
154C ARG 3.5 3.8 - - - -
155C LEU* 3.1 34.0 - - + +
193C GLY 4.7 0.8 + - - -
194C ASP* 3.5 0.4 + - - -
----------------------------------------------------------
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