Contacts of the strand formed by residues 86 - 95 (chain G) in PDB entry 1Y1V
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 VAL 86 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D GLN* 2.8 24.0 + - - +
183D LEU* 3.3 20.8 - - + +
194D LEU* 3.1 47.5 + - + +
84G GLY 4.0 6.1 - - - +
85G GLU* 1.3 75.6 - - - +
87G VAL* 1.3 62.1 + - - +
144G ARG* 3.8 13.7 - - + -
145G VAL 3.1 18.4 - - - +
146G LYS* 4.6 14.4 - - + -
168G LEU* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D TYR* 4.4 3.4 - - - +
179D GLN* 4.8 5.2 - - - +
183D LEU* 5.0 1.3 - - - -
1G MET* 5.6 0.9 - - + -
79G PHE* 5.5 4.0 - - + -
85G GLU* 3.0 28.9 + - + +
86G VAL* 1.3 80.1 - - - +
88G ASP* 1.3 57.9 - - - +
103G VAL* 3.4 35.8 - - + +
106G MET* 5.2 2.9 - - + -
108G VAL* 5.3 1.8 - - + -
144G ARG* 4.2 2.5 - - - -
145G VAL* 2.7 40.1 + - + +
147G ILE* 4.0 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 88 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 4.7 6.6 - - - +
147D TYR* 2.6 39.2 + - - -
151D PHE* 4.1 15.5 - - + +
182D SER 4.9 1.4 - - - +
183D LEU* 3.8 12.1 - - - +
87G VAL* 1.3 75.1 - - - +
89G GLY* 1.3 56.9 + - - +
103G VAL* 3.4 4.3 - - - +
143G ILE 3.0 17.9 - - - +
144G ARG* 3.3 41.8 + - + -
145G VAL 4.3 0.4 - - - +
171G ILE* 4.2 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 89 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D TYR* 3.7 1.6 - - - -
151D PHE* 3.5 16.5 - - - -
88G ASP* 1.3 74.1 - - - +
90G THR* 1.3 59.8 + - - -
101G VAL* 3.4 11.1 - - - +
102G GLN 3.4 13.9 - - - -
103G VAL* 3.7 5.0 - - - +
142G ARG* 3.4 5.2 - - - +
143G ILE 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 90 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D PHE* 3.2 23.8 - - - -
89G GLY* 1.3 73.5 - - - -
91G VAL* 1.3 72.2 + - - +
92G VAL* 3.9 1.1 - - - +
101G VAL* 3.8 1.6 - - - -
102G GLN* 2.6 43.0 + - - +
140G LYS* 3.4 33.2 - - + +
141G SER 4.0 2.9 - - - +
142G ARG* 4.5 7.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G THR* 1.3 85.5 - - - +
92G VAL* 1.3 74.0 + - - +
93G SER 3.6 14.6 - - - +
94G CYS* 5.3 0.9 - - + -
99G PHE* 3.8 21.1 - - + -
100G GLU 3.4 12.8 - - - +
101G VAL* 3.8 4.9 - - + +
137G ILE* 4.4 1.8 - - + -
138G THR 3.5 15.9 - - - +
139G ILE* 2.9 24.0 - - - +
140G LYS* 4.8 0.9 - - - +
141G SER* 2.8 24.4 + - - +
143G ILE* 3.5 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G THR* 3.9 9.9 - - - +
91G VAL* 1.3 83.3 - - - +
93G SER* 1.3 67.7 + - - +
100G GLU* 2.8 21.0 + - + +
102G GLN* 3.9 26.9 - - + +
107G LYS* 5.3 11.0 - - + +
139G ILE* 3.4 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G VAL* 3.6 4.2 - - - +
92G VAL* 1.3 84.8 - - - +
94G CYS* 1.3 65.1 + - - +
99G PHE* 3.5 3.8 - - - +
100G GLU* 2.9 55.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 94 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G VAL* 5.3 2.7 - - + -
93G SER* 1.3 80.7 - - - +
95G SER* 1.3 68.5 + - - +
98G GLY 4.0 0.7 - - - -
99G PHE* 4.0 14.8 - - + +
121G PHE* 4.5 7.2 - - - -
128G PRO* 4.3 35.2 - - + +
129G SER* 4.5 1.3 - - - -
130G TYR* 3.4 34.8 - - - -
137G ILE* 5.2 3.4 - - - -
138G THR* 5.8 0.9 - - - -
139G ILE* 5.5 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G CYS* 1.3 79.0 - - - +
96G GLN* 1.3 58.5 + - - +
97G HIS* 2.9 22.3 + - - +
98G GLY 3.1 13.1 + - - -
109G PHE* 5.5 0.5 - - - -
121G PHE* 3.5 10.8 - - - -
128G PRO* 5.8 0.7 - - - -
130G TYR* 2.5 34.1 + - - -
----------------------------------------------------------
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