Contacts of the strand formed by residues 119 - 125 (chain g) 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 GLU 119 (chain g).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115g TYR* 3.2 9.0 - - - -
116g ALA 3.2 30.0 + - - +
117g ASP* 3.2 12.6 - - + +
118g GLY* 1.3 92.3 - - - +
120g SER* 1.3 67.7 + - - +
121g PHE* 3.9 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 120 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15g LYS* 3.3 34.5 + - - -
16g PHE 3.2 11.3 + - - -
18g GLY 4.2 2.1 + - - -
19g GLY* 3.0 29.2 + - - -
20g VAL* 3.8 13.0 - - - -
114g GLY 3.6 4.7 - - - -
115g TYR* 4.0 2.3 - - - -
119g GLU* 1.3 81.0 + - - +
121g PHE* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 121 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15g LYS* 3.9 1.8 - - - +
20g VAL* 3.7 4.9 - - - +
85g PRO* 3.7 30.5 - - + -
86g ARG* 3.4 39.0 - - + -
89g HIS* 3.6 44.0 - + + -
112g ILE* 3.9 13.2 - - + -
113g GLY* 3.2 5.4 - - - -
114g GLY 2.9 39.8 + - - +
119g GLU 3.9 1.8 + - - +
120g SER* 1.3 75.0 - - - +
122g LEU* 1.3 64.7 + - - +
123g GLY* 3.8 17.5 - - - -
133g GLU* 3.4 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13g GLY* 3.6 33.4 - - - +
14g VAL* 3.7 4.5 - - - +
15g LYS* 3.7 16.4 - - + +
20g VAL* 4.0 21.5 - - + -
22g ILE* 4.7 0.9 - - + -
111g VAL* 3.7 20.2 - - + -
112g ILE 3.3 13.2 - - - +
113g GLY* 4.0 1.8 - - - -
121g PHE* 1.3 80.8 - - - +
123g GLY* 1.3 58.4 - - - +
133g GLU* 3.4 6.9 - - - +
134g ALA 3.2 41.8 + - - +
135g PRO 3.7 13.9 - - - +
136g SER* 3.9 4.7 - - - -
137g LEU* 3.6 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 123 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89g HIS* 3.7 19.4 - - - -
110g MET 3.7 0.5 - - - +
111g VAL* 3.3 5.0 - - - -
112g ILE 2.9 33.3 + - - -
121g PHE* 3.8 7.2 - - - -
122g LEU* 1.3 75.8 - - - +
124g TYR* 1.3 59.8 + - - -
132g TYR 3.2 10.3 - - - -
137g LEU* 3.3 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 124 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31f GLU* 5.7 0.2 + - - -
36f HIS* 3.8 21.0 - + - -
89g HIS* 3.3 3.0 + - - -
109g THR* 3.4 32.7 - - + +
110g MET 3.5 5.8 - - - -
111g VAL* 4.9 0.9 - - + -
123g GLY* 1.3 73.5 - - - -
125g VAL* 1.3 61.3 + - - +
126g ASP* 3.7 31.6 + - - -
130g VAL* 3.8 8.1 - - + -
131g ALA* 3.0 5.5 - - - -
132g TYR* 2.9 64.6 + + + +
137g LEU* 3.7 27.6 - - + +
138g ALA 4.7 9.0 - - - -
139g THR* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89g HIS* 3.4 35.7 - - + +
92g LEU* 4.1 13.5 - - + +
93g THR* 3.8 30.1 - - + +
96g MET* 3.7 20.0 - - + -
108g ASN 4.2 0.5 - - - +
109g THR* 3.7 6.1 - - - +
110g MET* 2.9 42.7 + - + +
112g ILE* 4.8 1.3 - - + -
124g TYR* 1.3 76.5 - - - +
126g ASP* 1.3 73.8 + - - +
129g GLY* 5.1 1.3 - - - -
130g VAL 3.5 2.9 - - - +
131g ALA* 4.3 1.6 - - + +
----------------------------------------------------------
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