Contacts of the strand formed by residues 133 - 143 (chain F) in PDB entry 6GJH
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 TYR 133 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E ARG* 3.4 5.6 - - - +
141E LYS* 3.1 44.1 + - + -
126F GLU* 4.0 32.1 - - + +
127F ARG* 3.5 9.0 - - - -
128F GLN* 3.4 48.2 + - + -
132F GLY* 1.3 73.2 - - - -
134F ILE* 1.3 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 134 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E PHE* 4.3 17.0 - - + -
139E THR 3.2 13.7 - - - +
140E ARG* 3.3 31.6 - - + +
124F HIS* 3.4 8.3 - - + -
126F GLU* 3.4 7.6 - - - +
127F ARG* 3.1 31.0 + - + +
129F ASP* 3.7 25.1 - - + +
133F TYR* 1.3 77.4 - - - +
135F SER* 1.3 75.9 + - - +
136F ARG* 3.6 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 135 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E PHE* 3.2 5.6 - - - -
139E THR* 3.0 44.4 + - - -
124F HIS* 3.7 17.5 - - - -
125F GLU* 4.6 0.7 - - - -
126F GLU* 4.0 18.5 - - - +
134F ILE* 1.3 75.7 - - - +
136F ARG* 1.3 68.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E CYS* 3.5 8.1 - - - +
138E PHE* 4.5 5.8 - - + +
140E ARG* 3.7 3.4 - - - +
103F HIS* 3.5 54.0 + - - +
104F PHE* 3.7 16.7 - - + -
123F LYS* 3.4 4.3 - - - +
124F HIS* 3.2 60.4 + - - +
129F ASP* 3.7 19.4 + - - +
134F ILE* 3.6 37.9 - - + +
135F SER* 1.3 83.8 - - - +
137F CYS* 1.3 62.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 137 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E LYS* 5.0 6.1 - - - -
136E ARG* 3.5 2.0 - - - +
137E CYS* 2.0 78.5 + - - +
104F PHE* 4.8 0.9 - - - -
122F GLY 3.3 11.7 - - - +
123F LYS* 4.2 21.5 - - + -
136F ARG* 1.3 76.9 - - - +
138F PHE* 1.3 67.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 138 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E ILE* 4.1 12.8 - - + -
135E SER* 3.1 13.9 - - - +
136E ARG* 4.5 7.4 - - + -
99F LEU* 4.2 12.1 - - + -
101F VAL* 3.9 22.2 - - + -
104F PHE* 3.7 33.2 - + + -
109F LEU* 4.1 11.2 - - + -
120F ILE* 3.8 26.7 - - + -
121F THR* 3.4 1.6 - - - -
122F GLY* 3.0 54.2 + - - +
137F CYS* 1.3 79.0 - - - +
139F THR* 1.3 73.1 + - - +
140F ARG* 3.9 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E GLU* 5.5 2.8 - - - +
133E TYR 3.9 0.3 - - - +
134E ILE* 3.3 5.1 - - - -
135E SER* 2.9 44.2 + - - +
119F GLU* 3.9 31.9 - - + +
120F ILE 3.3 4.3 - - - -
121F THR* 3.6 16.1 - - + +
138F PHE* 1.3 77.9 + - - +
140F ARG* 1.3 62.1 + - - +
141F LYS* 4.5 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E ASP* 3.0 40.2 + - - -
131E HIS* 3.8 17.7 + - - +
132E GLY 4.1 3.0 - - - +
133E TYR 3.2 10.5 + - - +
134E ILE* 3.5 34.0 - - + +
136E ARG* 4.2 9.1 - - - +
84F GLY* 4.0 16.0 + - - +
86F SER* 5.4 0.4 - - - -
99F LEU* 4.1 21.9 - - + +
118F VAL 3.8 0.5 - - - +
119F GLU* 3.7 1.4 - - - +
120F ILE* 2.8 36.6 + - + +
138F PHE* 3.9 12.0 - - + -
139F THR* 1.3 74.5 - - - +
141F LYS* 1.3 66.4 + - - +
142F TYR* 3.3 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E GLU* 3.0 36.2 + - - +
132E GLY* 3.6 7.3 - - - -
133E TYR* 2.8 45.1 + - + +
117F VAL* 3.9 18.6 - - + -
118F VAL 3.2 7.9 - - - +
119F GLU* 3.3 34.8 + - + -
139F THR* 4.5 9.0 - - + -
140F ARG* 1.3 79.9 - - - +
142F TYR* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 142 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131E HIS* 3.6 28.0 - - + -
132E GLY* 5.3 0.4 - - - -
133E TYR* 6.3 0.4 - - - -
86F SER* 2.8 37.1 + - - -
95F TRP* 4.0 24.0 - + + -
97F VAL* 4.1 30.9 - - + +
99F LEU* 4.0 10.5 - - + +
117F VAL* 3.4 7.2 - - - +
118F VAL* 2.9 39.3 + - + +
120F ILE* 3.8 28.3 - - + -
140F ARG* 3.3 29.1 - - + -
141F LYS* 1.3 76.3 - - - +
143F THR* 1.3 62.2 + - - +
144F LEU 3.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131E HIS 5.6 0.4 + - - -
132E GLY* 6.0 0.8 - - - -
133E TYR* 4.7 15.6 - - - -
95F TRP* 4.2 13.0 + - - -
116F GLY 4.0 7.0 - - - +
117F VAL* 4.8 10.1 - - + +
142F TYR* 1.3 74.1 - - - +
144F LEU* 1.3 73.8 + - - +
145F PRO* 4.1 1.0 - - - +
----------------------------------------------------------
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