Contacts of the strand formed by residues 102 - 106 (chain F) in PDB entry 6G2T
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 102 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F LEU* 3.2 13.0 - - + +
9F ILE* 4.0 27.4 - - + -
89F PHE* 4.1 13.9 - - + -
97F PRO* 6.0 1.8 - - + -
100F HIS 4.6 2.7 - - - +
101F PRO* 1.3 74.4 - - - +
103F LEU* 1.3 68.5 + - - +
104F LEU* 4.1 4.5 + - + +
122F MET* 4.0 23.8 - - + -
128F THR* 4.1 13.2 - - + +
130F ALA 3.2 7.6 + - - +
131F MET* 3.1 38.2 - - + +
132F TYR 3.1 3.8 + - - +
355F TRP* 3.5 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F LEU 2.7 13.7 + - - +
8F VAL* 3.7 10.2 - - + +
9F ILE* 2.8 31.7 + - - +
102F VAL* 1.3 73.4 - - - +
104F LEU* 1.3 71.0 + - - +
132F TYR* 3.3 45.3 - - + +
134F ALA* 4.4 5.6 - - + -
139F LEU* 4.5 5.4 - - + -
342F GLY* 3.3 42.0 - - - +
345F LEU* 4.0 14.4 - - + -
346F ALA* 4.9 3.8 - - + +
351F PHE* 4.2 6.5 - - + -
355F TRP* 3.7 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ILE* 3.6 41.3 - - + +
11F ASN* 4.8 4.3 - - + +
85F TRP* 4.4 13.2 - - + +
102F VAL* 4.6 5.8 - - + +
103F LEU* 1.3 81.7 - - - +
105F THR* 1.3 61.6 + - - +
118F MET* 3.6 34.8 - - + -
122F MET* 3.6 34.5 - - + -
131F MET* 3.6 13.2 - - + -
132F TYR 2.9 10.5 + - - +
133F VAL* 3.3 8.9 - - + -
134F ALA* 3.0 24.1 + - - +
139F LEU* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ILE 3.5 6.5 + - - -
10F ASP* 3.3 30.5 - - - +
11F ASN* 3.5 24.3 + - - +
104F LEU* 1.3 75.1 - - - +
106F GLU* 1.3 64.6 + - - +
118F MET* 4.9 9.5 - - - +
134F ALA 3.4 4.5 + - - -
135F ILE 4.2 0.5 - - - -
136F GLN* 3.1 43.1 + - + +
139F LEU* 4.2 11.5 - - - +
338F VAL* 3.7 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F THR* 1.3 77.8 + - - +
107F ALA* 1.3 58.3 + - - +
110F ASN* 3.1 44.7 + - - +
114F ASN* 4.1 4.9 - - - +
115F ARG* 3.4 54.5 + - + +
118F MET* 4.2 16.0 - - + +
133F VAL* 4.8 15.0 - - + -
134F ALA 2.6 18.7 + - - +
135F ILE* 3.1 8.3 - - + +
136F GLN* 2.7 37.0 + - - +
374F PHE* 6.2 0.2 - - - +
----------------------------------------------------------
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