Contacts of the strand formed by residues 53 - 61 (chain H) in PDB entry 6C6U
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 GLY 53 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H MET 3.8 0.2 + - - -
52H PRO* 1.3 76.0 - - - +
54H CYS* 1.3 65.8 + - - -
148H ARG* 3.3 14.4 - - - +
149H GLY 3.0 31.9 + - - +
177H TYR* 3.3 19.4 + - - +
179H PRO* 5.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 54 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H GLY* 1.3 80.3 - - - -
55H ALA* 1.3 65.2 + - - +
89H ALA* 5.5 0.7 - - - -
90H VAL* 3.2 25.7 + - - +
91H ARG* 5.2 0.7 - - - -
92H VAL* 3.7 35.2 - - + -
95H LYS 5.3 0.2 - - - -
96H ASP 5.3 1.1 - - - -
146H VAL* 5.3 2.0 - - + -
147H GLN 4.5 1.1 - - - +
148H ARG* 3.5 53.6 - - - +
176H CYS 4.5 2.1 - - - +
177H TYR* 3.8 5.1 + - - +
210H THR* 5.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H CYS* 1.3 76.7 - - - +
56H VAL* 1.3 67.0 + - - +
57H THR* 4.0 1.1 + - - -
88H LEU 5.0 9.2 - - - +
90H VAL* 5.3 3.4 - - - +
146H VAL* 3.1 10.5 - - - +
147H GLN 3.0 32.1 + - - +
175H ALA* 4.8 0.2 - - - -
176H CYS* 3.3 45.1 - - - +
177H TYR* 4.1 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H ALA* 1.3 75.6 - - - +
57H THR* 1.3 62.0 + - - +
58H GLU 4.2 3.4 - - - +
59H VAL* 3.7 29.4 - - + -
85H LEU* 4.0 20.0 - - + +
88H LEU* 4.0 18.8 + - + +
90H VAL* 5.1 0.9 - - + -
144H ILE* 3.8 21.5 - - + -
145H LYS 3.2 12.6 - - - +
146H VAL* 3.7 17.0 - - + -
173H VAL* 3.8 18.2 - - + +
175H ALA* 3.6 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H ALA 3.6 2.6 + - - -
56H VAL* 1.3 75.9 + - - +
58H GLU* 1.3 70.7 + - + +
145H LYS* 2.9 12.8 + - - -
147H GLN* 3.4 40.1 + - - +
158H ARG* 5.6 12.6 - - + +
172H LEU* 4.2 1.4 - - - +
173H VAL* 3.0 35.9 + - - +
175H ALA* 4.5 3.8 - - + +
177H TYR* 3.9 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H VAL* 4.0 0.4 - - - +
57H THR* 1.3 88.5 - - + +
59H VAL* 1.3 63.1 + - - +
60H GLU* 4.2 3.6 - - + +
143H ARG 3.6 2.1 - - - +
145H LYS* 3.1 63.1 + - + +
170H ARG* 3.3 42.8 + - + -
171H LEU 3.3 19.3 - - - +
172H LEU* 4.7 7.0 - - + +
173H VAL* 4.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H VAL* 3.7 22.7 - - + -
58H GLU* 1.3 79.1 - - - +
60H GLU* 1.3 59.9 + - - +
61H ILE* 4.1 9.6 - - + -
82H LEU* 4.7 5.8 - - + -
85H LEU* 3.8 22.2 - - + -
142H MET* 3.8 37.7 - - + -
143H ARG 3.4 7.2 - - - +
144H ILE* 3.8 11.0 - - + -
171H LEU* 3.2 35.1 + - - +
173H VAL* 4.3 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H GLU* 4.2 3.8 - - + -
59H VAL* 1.3 71.8 - - - +
61H ILE* 1.3 65.7 + - - +
99H ILE* 5.5 3.8 - - - +
142H MET* 3.8 0.5 - - - -
143H ARG* 3.0 60.1 + - + +
169H GLY 3.3 27.2 - - - +
170H ARG* 3.8 34.6 + - + +
171H LEU* 4.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H VAL* 3.9 11.6 + - + -
60H GLU* 1.3 78.7 - - - +
62H ASP* 1.3 68.7 + - - +
63H GLY 3.2 1.5 + - - +
64H VAL* 3.7 41.0 + - + +
71H LYS* 3.4 36.1 - - - +
78H ILE* 5.2 7.0 - - + -
81H ILE* 6.0 4.9 - - + -
82H LEU* 6.6 0.2 - - + -
140H ILE* 5.6 1.8 - - + -
141H SER 3.4 13.0 - - - +
142H MET* 3.7 31.6 - - + -
169H GLY 4.5 3.1 - - - +
171H LEU* 4.2 17.6 - - + +
----------------------------------------------------------
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