Contacts of the strand formed by residues 135 - 142 (chain A) in PDB entry 5GQQ
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 MET 135 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG 3.7 0.5 - - - +
42A HIS* 3.2 7.0 + - - -
43A TYR* 2.8 49.2 + - + -
132A ARG* 3.7 28.5 - - - +
133A ALA 4.0 7.0 - - - +
134A GLU* 1.3 77.8 - - - +
136A THR* 1.3 64.3 + - - +
137A VAL* 3.8 16.7 + - + -
175A TYR* 3.8 33.2 - - + -
193A TRP* 4.0 22.9 - - + -
195A ILE* 4.8 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PRO* 4.9 6.4 - - + +
40A ILE* 3.8 24.5 - - + -
41A ARG 3.4 11.0 - - - +
42A HIS* 2.9 24.9 + - - +
135A MET* 1.3 74.6 - - - +
137A VAL* 1.3 66.7 + - - +
138A PHE* 5.3 0.4 - - + -
195A ILE* 3.7 3.9 - - - +
196A GLN* 2.8 56.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLU 3.8 0.3 - - - +
40A ILE* 3.6 5.4 - - - +
41A ARG* 2.9 35.8 + - + +
43A TYR* 3.8 28.9 - - + -
135A MET* 3.8 32.5 - - + -
136A THR* 1.3 79.8 - - - +
138A PHE* 1.3 65.7 + - - +
139A VAL* 3.8 18.1 + - + +
175A TYR* 4.9 0.2 - - + -
193A TRP* 4.0 20.2 - - + -
194A LEU 3.2 11.4 - - - +
195A ILE* 4.2 12.8 - - + -
196A GLN 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 3.8 20.9 - + + -
39A GLU 3.5 2.0 - - - -
40A ILE* 3.9 30.5 - - + -
136A THR* 5.3 0.2 - - + -
137A VAL* 1.3 74.9 - - - +
139A VAL* 1.3 60.0 + - - +
158A LEU* 3.4 7.1 - - + +
162A LEU* 3.8 33.4 - - + -
167A LYS* 4.0 28.5 - - + -
168A VAL 3.8 12.6 - - - -
169A PHE* 4.2 9.0 - - + -
193A TRP* 3.2 5.4 - - - -
194A LEU 2.6 41.4 + - - +
196A GLN* 3.6 46.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 3.3 10.1 - - - +
39A GLU* 2.8 42.3 + - + +
41A ARG* 3.8 31.4 - - + +
137A VAL* 3.8 17.7 - - + +
138A PHE* 1.3 76.5 - - - +
140A ARG* 1.3 64.7 + - - +
141A SER* 4.7 1.8 - - - +
158A LEU* 4.5 0.4 - - - -
191A GLU* 3.5 38.4 - - + +
192A VAL 3.6 2.7 - - - -
193A TRP* 3.5 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLY 4.8 5.9 + - - -
37A SER 3.9 17.5 + - - +
38A TYR* 5.1 0.2 - - - +
138A PHE 4.2 0.2 + - - -
139A VAL* 1.3 75.8 - - - +
141A SER* 1.3 72.4 + - - +
142A PHE* 4.1 1.4 - - - -
154A GLN* 2.6 52.1 + - + +
157A THR* 3.6 25.9 - - - +
158A LEU* 3.5 28.3 - - + +
161A ILE* 3.8 16.8 - - - +
191A GLU* 3.3 2.1 - - - -
192A VAL* 3.0 39.3 + - + +
75D GLU* 5.5 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 4.2 2.3 - - - +
140A ARG* 1.3 87.8 + - - +
142A PHE* 1.3 64.6 + - - +
154A GLN* 4.8 0.2 - - - +
189A ASN* 4.0 19.7 + - - +
190A ASN 3.3 11.7 - - - -
191A GLU* 4.1 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG 4.1 5.4 - - - -
141A SER* 1.3 79.1 - - - +
143A ASP* 1.3 76.8 + - - +
144A GLY 4.0 2.9 + - - +
145A PHE 4.1 17.3 - - - -
146A SER* 4.0 5.4 - - - -
150A LYS* 3.9 18.4 - - + -
151A ASN* 3.6 20.0 - - - -
154A GLN* 3.8 38.6 - - + +
189A ASN* 3.4 22.5 - - - +
190A ASN* 3.1 35.9 + - + -
191A GLU 3.8 23.3 - - - -
192A VAL* 3.9 12.1 - - + -
----------------------------------------------------------
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