Contacts of the strand formed by residues 113 - 118 (chain A) in PDB entry 5G04
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 113 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.4 29.2 - - + -
27A HIS* 3.7 26.9 - - + +
101A ILE* 3.5 29.4 - - + -
102A TRP 4.0 3.1 - - - +
103A SER* 4.4 1.1 - - - +
104A LYS* 5.7 0.2 - - - -
112A ALA* 1.3 73.8 - - - +
114A TYR* 1.3 60.0 + - - +
115A LYS* 4.2 13.5 - - - +
116A ALA* 5.0 0.4 - - + +
265O GLN* 3.4 36.9 + - + +
500O ASN 4.5 4.7 - - - +
501O SER 5.5 2.0 - - - +
502O GLN* 6.4 0.2 - - - -
505O GLN* 3.9 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TRP* 2.7 76.2 + + + +
104A LYS* 3.5 44.6 - - + -
112A ALA 3.5 2.4 + - - -
113A VAL* 1.3 72.3 - - - +
115A LYS* 1.3 87.7 + - + +
164A ILE* 4.9 12.1 + - + +
265O GLN* 3.4 15.8 + - - +
314O PHE 5.5 1.3 + - - -
316O HIS* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ILE* 3.8 1.9 - - - +
102A TRP* 3.1 29.7 + - - +
113A VAL* 3.7 4.8 - - - -
114A TYR* 1.3 117.9 + - + +
116A ALA* 1.3 60.8 + - - +
117A PHE* 3.3 27.5 - - + -
162A HIS* 3.2 13.9 + - + -
163A SER 4.1 5.1 + - - -
164A ILE* 4.4 3.8 + - - +
265O GLN* 3.6 9.9 - - + -
267O VAL* 3.4 24.2 - - + -
314O PHE* 3.9 21.3 - - + -
316O HIS* 2.9 35.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 4.9 2.7 - - + -
31A HIS* 3.3 37.2 - - + +
99A MET* 5.8 0.7 - - + -
100A VAL 3.7 2.7 - - - -
101A ILE* 4.0 11.4 - - + -
113A VAL* 5.1 0.7 - - + -
115A LYS* 1.3 74.4 - - - +
117A PHE* 1.3 63.7 + - - +
264O VAL 4.0 1.6 - - - +
265O GLN* 2.7 21.0 + - + +
266O ASP* 2.9 19.2 - - - +
267O VAL* 3.0 16.1 + - - +
268O PHE 3.7 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASN 3.6 2.9 - - - +
99A MET* 3.3 2.8 - - - +
100A VAL* 2.5 46.7 + - - +
102A TRP* 3.8 15.0 - + + -
115A LYS* 3.3 43.5 - - + -
116A ALA* 1.3 72.9 - - - +
118A THR* 1.3 57.7 + - - +
119A VAL* 4.3 3.7 - - - +
151A ILE* 3.8 23.8 - - + -
153A ILE* 3.5 26.4 - - + +
162A HIS* 3.5 35.7 - - + -
267O VAL* 3.5 22.0 - - + -
268O PHE* 3.9 23.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A HIS* 4.9 0.7 - - - +
32A PRO* 5.4 0.2 - - + -
33A ASN* 3.9 24.9 - - - +
35A LEU* 4.1 25.6 - - + +
98A ASN* 3.5 3.4 - - + +
99A MET* 3.5 30.0 - - + +
116A ALA 3.8 0.8 + - - -
117A PHE* 1.3 68.8 - - - +
119A VAL* 1.3 63.4 + - - +
120A ASP* 3.8 1.5 - - - +
266O ASP* 2.2 40.1 + - - +
268O PHE* 3.3 22.2 - - - +
269O SER* 3.8 6.6 + - - -
272O HIS* 5.3 2.8 - - - -
----------------------------------------------------------
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