Contacts of the strand formed by residues 126 - 136 (chain E) in PDB entry 2CFX
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 ALA 126 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E ALA* 4.0 14.6 - - + -
72E THR 3.2 16.8 - - - +
73E VAL* 4.3 0.2 - - - -
74E LYS* 4.1 8.8 - - - +
81E PHE* 3.6 28.5 - - + -
122E THR* 3.2 10.3 + - - +
123E SER* 3.5 21.1 + - - -
124E PRO 3.7 1.2 - - - -
125E TYR* 1.3 83.7 - - - +
127E GLN* 1.3 61.9 + - - +
128E THR* 3.7 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C GLN* 5.7 3.1 + - - -
70E GLU 3.5 0.5 - - - +
71E ALA* 3.2 4.0 - - - -
72E THR* 2.7 60.6 + - + +
74E LYS* 3.4 35.5 - - - +
123E SER* 5.6 1.6 - - - +
126E ALA* 1.3 73.1 - - - +
128E THR* 1.3 60.3 + - - +
72G THR* 6.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E VAL* 3.6 24.7 - - + -
70E GLU 3.0 5.6 - - - +
71E ALA* 4.5 8.3 - - + -
118E PHE* 5.5 0.7 - - + -
119E ILE* 3.5 35.0 - - + +
122E THR* 3.6 25.4 - - + +
123E SER* 5.8 1.3 - - - -
126E ALA 3.7 7.6 + - - +
127E GLN* 1.3 82.7 - - - +
129E VAL* 1.3 67.1 + - - +
130E THR* 4.1 1.2 + - - -
99G GLY 3.9 7.0 - - - +
100G ALA 4.2 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ILE 3.8 0.5 - - - +
69E VAL* 3.3 4.4 - - - -
70E GLU* 2.8 54.4 + - + +
72E THR* 6.5 0.9 - - + -
128E THR* 1.3 77.9 - - - +
130E THR* 1.3 63.1 + - - +
131E HIS* 3.6 26.3 - - + +
99G GLY* 3.5 22.7 - - - -
100G ALA* 3.7 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D PHE* 4.3 9.0 - - + -
67E CYS* 3.7 30.3 - - + -
68E ILE 3.5 3.6 - - - +
69E VAL* 4.3 6.6 - - + +
115E VAL* 3.9 14.8 - - + -
119E ILE* 3.0 29.7 - - + +
128E THR* 4.5 2.3 + - - -
129E VAL* 1.3 75.6 - - - +
131E HIS* 1.3 65.4 + - - +
132E VAL* 4.1 0.8 + - + +
98F ALA 5.0 0.5 - - - +
98G ALA* 3.9 16.5 - - + +
99G GLY* 3.3 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E CYS* 3.2 3.0 - - - -
68E ILE* 2.6 54.1 + - + +
70E GLU* 2.5 38.2 + - + +
129E VAL* 3.6 23.4 - - + +
130E THR* 1.3 74.9 + - - +
132E VAL* 1.3 63.3 + - - +
133E ILE 3.5 0.2 + - - -
70F GLU* 6.2 0.9 - - - -
97F ILE* 4.0 24.2 - - + +
98F ALA 3.4 23.6 + - - +
99F GLY* 4.5 7.8 - - - -
100F ALA 5.3 2.9 + - - -
101F ALA 6.2 0.9 - - - -
104F MET* 3.9 19.9 - - + +
99G GLY* 5.8 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D LEU* 3.9 32.8 - - + -
132D VAL* 4.1 22.4 - - + -
134D PHE* 4.8 1.8 - - + -
65E VAL* 5.3 1.6 - - + -
66E SER 3.9 8.7 - - - +
67E CYS* 4.0 15.5 - - - -
112E LEU* 4.2 19.5 - - + -
130E THR* 4.1 0.8 + - + -
131E HIS* 1.3 71.4 - - - +
133E ILE* 1.3 73.9 + - - +
134E PHE* 3.7 2.3 + - + -
97F ILE* 3.4 2.5 - - - -
98F ALA* 2.8 40.4 + - + +
98G ALA* 4.4 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D LEU* 4.0 8.8 - - - +
66E SER* 2.9 40.3 + - - +
67E CYS* 4.0 8.7 - - - -
68E ILE* 3.9 31.9 - - + -
106E LYS* 4.1 11.9 - - - -
132E VAL* 1.3 81.6 - - - +
134E PHE* 1.3 64.5 + - - +
135E SER* 3.4 26.0 - - - +
136E GLU* 5.4 0.2 - - + -
95F TYR* 3.9 35.4 - - + -
96F ARG 3.4 4.7 - - - +
97F ILE* 4.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D LEU* 3.5 49.2 - - + +
113D GLU* 4.8 7.1 + - - +
115D VAL* 3.6 31.2 - - + -
116D GLU* 3.6 26.6 - - + +
119D ILE* 4.5 15.5 - - + -
130D THR* 4.2 6.3 - - + -
132D VAL* 4.5 3.4 - - + -
132E VAL* 4.6 1.8 - - + -
133E ILE* 1.3 76.8 - - - +
135E SER* 1.3 60.1 + - - +
96F ARG* 2.7 26.3 + - + +
97F ILE 3.6 29.2 - - - -
98F ALA* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D GLU* 6.3 1.8 - - - -
116D GLU* 2.8 28.9 + - - -
133E ILE* 3.4 14.4 - - - +
134E PHE* 1.3 79.4 - - - +
136E GLU* 1.3 67.6 + - - +
95F TYR* 3.6 0.3 - - - -
96F ARG* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E ILE* 5.4 0.4 - - + -
135E SER* 1.3 82.2 + - - +
137E ILE* 1.3 73.5 + - - +
138E ASP* 3.7 5.4 + - - +
82F LYS* 5.6 1.7 + - - -
93F PHE* 4.7 8.1 - - - +
94F CYS 3.3 13.4 + - - +
95F TYR* 3.6 33.5 + - + +
96F ARG* 4.4 1.3 - - - +
----------------------------------------------------------
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