Contacts of the strand formed by residues 83 - 91 (chain H) in PDB entry 6H25
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 ILE 83 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H GLY 3.9 3.5 + - - +
82H ASP* 1.3 73.3 - - - +
84H VAL* 1.3 63.5 + - - +
143H ALA 3.5 5.8 - - - +
144H GLU* 4.6 3.1 - - + -
163H TYR* 3.4 39.0 - - + +
185H HIS* 3.6 27.4 - - + +
186H PHE* 4.6 15.3 - - + -
196H ILE* 4.8 9.9 - - + -
197H LEU 3.5 26.0 - - - +
198H GLY* 4.0 5.4 - - - -
199H ASN* 3.0 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H TYR* 4.8 12.6 - - + +
83H ILE* 1.3 77.1 - - - +
85H VAL* 1.3 70.3 + - - +
100H THR* 4.0 11.7 - - + -
141H ILE* 5.6 0.2 - - - +
142H SER* 3.2 6.3 - - - -
143H ALA 2.9 42.4 + - - +
145H VAL* 4.4 17.7 - - + -
156H LEU* 3.8 26.5 - - + -
198H GLY* 4.9 0.7 - - - -
199H ASN 4.8 0.9 - - - +
200H ASN* 3.4 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H VAL* 1.3 82.1 - - - +
86H GLY* 1.3 64.0 + - - +
100H THR* 3.4 4.2 - - - +
140H LEU* 5.1 2.5 - - + -
141H ILE 3.4 10.5 - - - +
142H SER* 4.3 8.1 - - - -
166H LEU* 4.6 14.4 - - + -
171H LEU* 4.5 13.7 - - + -
196H ILE* 3.9 30.5 - - + +
198H GLY* 4.8 6.5 - - - +
200H ASN* 3.1 26.3 + - - -
202H PHE* 3.1 35.7 - - + +
204H TRP* 4.8 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H VAL 4.3 0.2 - - - -
85H VAL* 1.3 76.4 - - - +
87H ARG* 1.3 59.9 + - - -
98H VAL* 3.8 17.9 - - - -
99H GLU 3.6 10.1 - - - -
100H THR* 3.9 2.5 - - - -
140H LEU* 3.4 10.1 - - - +
141H ILE* 2.9 38.0 + - - +
202H PHE* 4.0 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 87 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E VAL 4.6 11.7 - - - -
5E THR* 3.5 19.8 + - - +
6E LEU* 3.4 27.1 - - - +
10E GLU* 3.4 12.9 + - - -
86H GLY* 1.3 72.6 - - - -
88H ILE* 1.3 72.6 - - - +
89H THR* 3.6 3.7 + - + +
98H VAL* 3.5 1.7 - - - -
99H GLU* 2.8 51.8 + - + +
138H GLY* 3.9 10.4 + - - +
139H ASP 3.5 9.4 - - - +
140H LEU* 3.5 27.0 - - + +
171H LEU* 4.1 24.2 - - - +
173H GLN* 5.2 8.5 - - - +
202H PHE* 4.6 6.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E VAL 5.4 1.7 - - - +
87H ARG* 1.3 78.0 - - - +
89H THR* 1.3 62.6 + - - +
90H GLU 4.2 5.8 - - - +
91H VAL* 5.1 0.2 - - + -
96H TRP* 4.0 26.0 - - + +
97H LYS 3.7 9.6 - - - +
98H VAL* 4.5 8.1 - - + +
135H LEU* 3.7 34.1 - - + -
136H GLN 3.7 16.6 - - - +
137H GLU* 4.4 6.2 - - - +
138H GLY* 3.2 29.7 + - - +
139H ASP* 3.2 17.0 + - + +
141H ILE* 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H ARG* 4.0 4.0 - - + +
88H ILE* 1.3 78.0 - - - +
90H GLU* 1.3 69.7 + - - +
97H LYS* 2.9 28.2 + - - +
99H GLU* 3.7 31.6 - - + -
105H ASP* 5.0 5.3 + - + +
137H GLU* 3.2 29.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H ILE* 4.2 1.8 - - - +
89H THR* 1.3 86.8 + - - +
91H VAL* 1.3 66.9 + - - +
92H GLN* 3.8 8.1 - - + +
96H TRP* 3.7 8.7 - - - -
97H LYS* 3.3 37.3 + - + +
137H GLU* 4.9 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H ILE* 5.1 0.2 - - + -
90H GLU* 1.3 78.0 - - - +
92H GLN* 1.3 68.7 + - - +
96H TRP* 3.7 30.3 - - + +
131H MET* 4.1 17.3 - - + -
132H ARG* 4.1 38.1 - - + +
135H LEU 4.9 0.7 - - - +
137H GLU* 4.2 26.8 - - + +
----------------------------------------------------------
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