Contacts of the strand formed by residues 131 - 138 (chain C) in PDB entry 5GJQ
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 VAL 131 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL* 3.5 7.4 - - - +
75C TYR* 4.0 9.6 - - + -
76C SER 3.5 4.3 - - - +
77C GLY 4.6 1.3 - - - -
78C MET 3.1 29.2 - - - +
81C ASP* 3.5 20.2 - - + -
82C TYR* 3.8 7.4 - - + +
85C LEU* 4.3 13.0 - - + -
117C MET* 3.5 13.0 - - - +
129C PHE* 3.2 5.1 + - + -
130C GLY* 1.3 82.3 - - - +
132C SER* 1.3 76.8 + - - +
133C LEU* 3.7 22.7 - - + -
150C PRO* 3.2 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 4.9 2.6 - - - +
28C VAL* 3.4 22.4 - - - +
75C TYR* 3.2 6.9 - - - +
76C SER 2.9 33.1 + - - -
131C VAL* 1.3 74.6 - - - +
133C LEU* 1.3 62.0 + - - +
134C LEU* 5.9 0.4 - - - +
147C GLN* 3.8 16.3 + - - -
148C SER 3.3 11.6 + - - -
149C ASP* 3.6 17.8 - - - +
150C PRO* 3.9 3.6 - - - +
162C MET* 4.9 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LEU* 3.9 24.5 - - + -
74C VAL 3.5 3.1 - - - +
75C TYR* 4.1 0.4 - - + -
82C TYR* 3.6 36.3 - - + -
85C LEU* 4.0 24.5 - - + -
113C VAL* 3.8 24.0 - - + -
117C MET* 4.1 2.9 - - - -
131C VAL* 3.7 16.8 - - + -
132C SER* 1.3 74.0 - - - +
134C LEU* 1.3 61.1 + - - +
135C ILE* 4.1 5.2 - - + -
147C GLN* 3.1 11.3 - - - +
148C SER* 2.9 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C SER* 4.4 15.3 - - - +
35C VAL 4.2 4.3 - - - -
36C GLY* 3.9 29.4 - - - +
45C LEU* 4.0 8.3 - - + +
72C GLY 3.8 0.2 - - - +
73C LEU* 3.3 5.7 - - - +
74C VAL* 2.9 55.4 + - + +
75C TYR* 4.9 0.6 - - - +
132C SER 4.3 0.6 + - - -
133C LEU* 1.3 74.7 - - - +
135C ILE* 1.3 61.6 + - - +
145C LEU* 4.2 7.6 - - + -
146C PHE 3.3 12.6 - - - +
147C GLN* 3.7 22.4 - - + -
160C THR* 3.8 23.1 - - + +
162C MET* 5.3 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ILE* 3.7 20.9 - - + -
72C GLY 3.3 12.6 - - - +
73C LEU* 3.5 21.3 - - + -
106C THR* 4.4 6.8 - - + +
109C LEU* 4.3 11.4 - - + -
110C VAL* 3.6 41.3 - - + +
113C VAL* 4.6 20.9 - - + -
133C LEU* 4.4 9.6 - - + +
134C LEU* 1.3 77.7 - - - +
136C CYS* 1.3 60.6 + - - +
144C TYR 3.8 0.5 - - - +
145C LEU* 3.4 5.2 - - - +
146C PHE* 2.9 36.2 + - - +
148C SER* 4.9 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C VAL* 3.7 27.1 - - + -
45C LEU* 3.6 26.0 - - + +
71C ILE* 3.2 8.1 - - - +
72C GLY 2.9 33.1 + - - -
106C THR* 4.1 3.4 - - - -
134C LEU 4.1 1.0 + - - -
135C ILE* 1.3 74.2 - - - +
137C GLY* 1.3 58.7 + - - +
144C TYR 3.2 5.2 - - - -
145C LEU* 4.5 1.1 - - + +
210C GLY 6.0 0.2 - - - -
211C ILE 5.3 0.4 - - - -
212C CYS* 3.6 24.9 - - - -
217C PHE* 3.6 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C VAL* 4.3 1.1 - - - +
70C HIS 3.3 10.1 - - - -
71C ILE* 4.1 0.7 - - - -
106C THR* 3.2 24.5 - - - +
136C CYS* 1.3 75.6 - - - +
138C TRP* 1.3 60.2 + - - +
139C ASN 4.0 0.6 + - - -
143C PRO* 3.6 3.3 - - - +
144C TYR* 2.9 35.6 + - - +
212C CYS* 3.5 9.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C HIS* 3.1 37.7 + - + +
106C THR* 4.0 0.4 + - - -
137C GLY* 1.3 72.1 - - - +
139C ASN* 1.3 59.8 + - - +
142C ARG 4.0 4.0 - - - -
143C PRO* 4.8 0.7 - - + -
212C CYS* 3.5 9.4 - - - +
213C ASN 3.5 20.9 - - - +
214C GLU* 3.1 31.0 - - - +
216C GLY* 5.8 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