Contacts of the strand formed by residues 131 - 141 (chain E) in PDB entry 6D6Q
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 HIS 131 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E MET* 4.5 19.3 - - + -
67E GLY 3.8 9.0 - - - -
69E PRO* 4.2 4.3 - - - +
125E CYS* 4.5 1.6 - - - -
126E ILE* 3.9 11.6 + - + -
127E SER* 3.0 34.0 + - - +
130E GLU* 1.3 100.5 + - + +
132E CYS* 1.3 66.1 + - - +
170E VAL* 3.6 33.5 - - + +
178E LYS* 3.6 38.1 + - + +
180E ILE* 5.8 3.2 - - + +
14K GLY 5.4 6.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E MET* 3.4 7.1 - - - +
67E GLY 2.9 37.0 + - - +
69E PRO* 3.8 19.7 - - + -
76E GLU* 3.7 7.0 - - - -
77E GLY* 3.1 37.2 - - - -
78E TYR* 6.0 0.2 - - + -
124E LEU 3.1 18.8 - - - -
125E CYS* 4.0 6.1 - - - -
126E ILE* 4.6 10.5 - - - +
131E HIS* 1.3 79.8 - - - +
133E TRP* 1.3 73.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 133 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E ALA* 4.0 21.1 - - + -
65E GLU 3.3 20.2 - - - -
66E MET* 3.6 20.6 - - + -
77E GLY* 3.7 11.8 - - - -
78E TYR* 3.8 1.3 + - - -
123E THR 4.8 3.0 + - - -
124E LEU* 3.0 60.4 + - + +
125E CYS 5.2 0.2 - - - -
126E ILE* 4.0 17.7 - - + +
132E CYS* 1.3 87.7 - - - +
134E VAL* 1.3 72.6 + - - +
135E LEU* 5.8 0.9 - - + -
165E ILE* 3.4 24.7 - - + +
166E PRO* 3.0 40.6 + - + -
168E VAL* 3.8 25.4 - - + -
190E ILE* 5.1 4.8 - - + +
16K VAL* 4.1 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E LYS 3.3 4.0 - - - +
64E ALA* 3.4 2.1 - - - -
65E GLU* 2.9 42.9 + - + +
66E MET 4.2 1.6 - - - +
67E GLY* 4.1 19.5 - - - +
78E TYR* 3.2 50.0 - - + +
80E GLU* 6.0 0.2 - - + -
132E CYS 4.5 0.4 - - - +
133E TRP* 1.3 82.6 - - - +
135E LEU* 1.3 63.3 + - - +
136E TYR* 3.2 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E VAL* 4.5 16.8 - - + -
63E LYS 3.6 2.0 - - - -
64E ALA* 4.0 25.6 - - + -
78E TYR 3.0 13.8 + - - +
79E LEU* 3.5 30.9 - - + -
80E GLU* 2.9 29.2 + - - +
119E VAL* 4.8 3.4 - - + -
124E LEU* 4.3 18.2 - - + -
133E TRP* 5.8 0.7 - - + -
134E VAL* 1.3 70.8 - - - +
136E TYR* 1.3 61.2 + - - +
137E VAL* 3.4 8.9 + - + +
160E LEU* 5.3 8.1 - - + -
163E THR* 4.7 4.5 - - + -
165E ILE* 4.0 17.0 - - + -
192E LEU* 4.1 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 136 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ARG* 3.3 46.9 - - - +
61E GLY 3.9 0.5 - - - +
62E VAL* 3.5 2.1 - - - -
63E LYS* 2.9 39.8 + - + +
65E GLU* 2.9 39.6 + - + -
67E GLY* 6.0 0.7 - - - -
78E TYR* 4.1 11.6 + + - -
80E GLU* 3.8 32.1 - - + -
134E VAL* 3.2 29.9 + - + +
135E LEU* 1.3 69.4 - - - +
137E VAL* 1.3 62.3 + - - +
138E ASP* 4.3 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ARG* 4.9 0.5 + - - -
60E VAL* 4.3 16.2 - - + -
61E GLY 3.5 8.5 - - - +
62E VAL* 4.1 19.1 - - + -
79E LEU* 5.1 3.4 - - + -
80E GLU 2.9 9.4 + - - +
81E PHE* 3.3 42.6 - - + -
82E PHE 2.9 22.3 + - - -
135E LEU* 4.1 10.8 - - + +
136E TYR* 1.3 72.7 - - - +
138E ASP* 1.3 74.0 + - - +
139E VAL* 4.1 9.6 - - + -
156E VAL* 4.7 6.7 - - + -
160E LEU* 4.8 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 2.4 33.5 + - + +
80B PHE* 3.7 30.9 + - + +
85B ARG* 3.4 31.7 + - - -
60E VAL* 3.5 2.3 - - - -
61E GLY 2.9 35.6 + - - +
63E LYS* 4.7 2.6 - - - +
82E PHE* 3.5 10.4 - - + +
136E TYR 4.4 5.9 - - - +
137E VAL* 1.3 91.3 - - - +
139E VAL* 1.3 66.2 + - - +
140E LEU 4.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PHE* 5.8 0.4 - - - -
58E ILE* 4.2 12.1 - - + -
59E LEU 3.7 8.3 - - - +
60E VAL* 4.3 11.2 - - + -
81E PHE* 5.3 0.2 - - + -
82E PHE* 2.9 15.3 + - - +
83E VAL* 3.6 19.5 - - + -
84E ASP* 2.9 27.1 + - - +
109E LEU* 4.3 17.3 - - + -
137E VAL* 4.4 10.5 - - + -
138E ASP* 1.3 76.9 - - - +
140E LEU* 1.3 66.9 + - - +
141E LEU* 4.2 5.2 - - + -
152E ILE* 4.1 33.4 - - + -
156E VAL* 4.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ALA* 4.7 2.5 - - + -
80B PHE* 4.1 17.7 - - + -
125B GLN* 4.1 22.0 - - + +
127B LEU* 3.2 35.2 - - + -
58E ILE* 3.7 4.0 - - - +
59E LEU* 2.9 47.6 + - + +
84E ASP* 3.5 37.7 - - + +
86E SER* 4.4 2.9 - - - -
139E VAL* 1.3 76.5 - - - +
141E LEU* 1.3 70.9 + - - +
142E LEU* 4.2 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E ASP 4.4 0.9 - - - -
58E ILE* 4.1 17.3 - - + -
83E VAL* 4.6 10.5 - - + -
84E ASP 3.0 13.8 + - - +
85E CYS* 3.7 37.2 - - + -
86E SER* 3.4 21.8 - - - +
89E ALA* 5.0 6.1 - - + -
101E LEU* 4.8 3.1 - - + -
102E GLY* 6.2 0.2 - - - -
105E ILE* 4.5 18.6 - - + -
139E VAL* 4.8 4.0 - - + -
140E LEU* 1.3 74.4 - - - +
142E LEU* 1.3 71.4 + - - +
143E GLU 4.7 6.7 - - - +
148E LEU* 3.6 33.4 - - + -
152E ILE* 4.4 10.1 - - + -
----------------------------------------------------------
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