Contacts of the strand formed by residues 84 - 93 (chain G) in PDB entry 5IYB
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 84 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D CYS* 3.9 17.1 - - - -
102D ASN* 6.0 0.7 - - - +
103D LEU* 3.6 37.4 - - + +
114D LEU* 4.2 30.1 - - + +
82G GLY 3.7 1.8 + - - +
83G GLU* 1.3 73.4 - - - +
85G VAL* 1.3 70.9 + - - +
144G ARG* 4.9 4.5 - - + -
145G LEU 3.4 13.5 - - - +
146G LYS* 3.6 36.8 - - + -
167G TYR 5.5 0.4 - - - +
168G LEU* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D TYR* 5.3 2.0 - - - +
102D ASN* 6.6 0.4 - - + -
103D LEU* 4.3 4.3 - - - -
77G PHE* 6.2 3.4 - - + -
79G PRO* 6.0 3.1 - - + -
83G GLU* 3.8 28.9 - - + +
84G VAL* 1.3 80.8 - - - +
86G ASP* 1.3 67.9 + - - +
87G ALA 3.9 0.3 + - - -
101G ILE* 4.0 28.0 - - + -
144G ARG* 3.6 1.3 - - - +
145G LEU* 2.9 53.1 + - + +
147G ILE* 4.2 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D TYR* 3.1 24.3 + - - +
71D PHE* 3.5 25.6 - - + +
73D ARG* 3.2 26.3 + - - -
102D ASN 4.1 9.4 - - - +
103D LEU* 3.8 15.9 - - - +
85G VAL* 1.3 74.5 - - - +
87G ALA* 1.3 59.8 + - - +
101G ILE* 3.6 6.1 - - - +
142G GLU* 6.1 0.2 - - + -
143G ILE 3.4 7.4 - - - +
144G ARG* 3.5 20.8 - - - +
171G VAL* 4.1 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D PHE* 4.1 3.5 - - - -
85G VAL 3.9 0.6 + - - +
86G ASP* 1.3 75.4 - - - +
88G VAL* 1.3 64.5 + - - +
99G THR* 3.4 30.3 - - + +
100G GLU 3.7 11.7 - - - +
101G ILE* 4.1 9.0 - - + -
142G GLU* 3.4 5.2 - - - -
143G ILE* 2.8 33.0 + - + +
145G LEU* 3.7 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D TYR* 5.3 3.6 - - + -
70D ARG* 3.2 42.0 - - - +
71D PHE* 3.5 26.9 - - + -
87G ALA* 1.3 75.4 - - - +
89G VAL* 1.3 75.5 + - - +
90G THR* 3.4 4.1 + - + +
99G THR* 3.1 3.8 - - - -
100G GLU* 2.7 42.3 + - + +
140G ASP* 3.7 4.5 - - - +
141G ASP 3.1 14.6 - - - +
142G GLU* 3.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G VAL* 1.3 72.6 - - - +
90G THR* 1.3 60.4 + - - +
91G GLN 3.8 19.3 - - - +
92G VAL* 4.6 1.3 - - + -
97G LEU* 3.8 31.6 - - + -
98G PHE 3.2 13.5 - - - +
99G THR* 4.0 1.3 - - + +
137G ILE* 3.9 17.9 - - + -
138G GLN 3.4 25.1 - - - +
140G ASP* 2.6 34.7 + - - -
141G ASP* 2.8 19.0 + - + +
143G ILE* 4.0 15.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
88G VAL* 3.9 12.6 - - + +
89G VAL* 1.3 77.0 - - - +
91G GLN* 1.3 65.4 + - - +
98G PHE* 3.1 29.2 + - - +
99G THR 4.3 1.7 + - - -
100G GLU* 4.0 28.7 - - + +
139G GLN* 3.6 22.0 + - - +
140G ASP 4.8 0.9 - - - +
145Q PHE* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G VAL* 3.8 2.8 - - - -
90G THR* 1.3 83.2 + - - +
92G VAL* 1.3 93.2 + - - +
93G ASN* 4.2 1.2 + - + -
96G GLY 4.3 0.2 - - - +
97G LEU* 3.8 8.7 - - - +
98G PHE* 3.2 46.1 + - + +
126G PRO* 5.8 0.9 - - - +
139G GLN* 2.5 38.7 + - - +
145Q PHE* 3.4 38.9 - - + -
147Q PRO* 4.9 5.7 + - - +
150Q GLY* 3.9 16.1 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
89G VAL* 4.6 1.6 - - + -
91G GLN* 1.3 86.8 + - - +
93G ASN* 1.3 61.1 + - - +
96G GLY 4.4 1.3 - - - -
97G LEU* 4.3 8.1 - - + -
119G PHE* 4.1 13.5 - - + -
126G PRO* 3.2 43.3 - - + +
127G CYS* 3.8 6.5 - - - +
128G TYR* 4.0 19.7 - - + -
137G ILE 4.0 19.1 - - - +
138G GLN* 4.5 13.7 - - - -
139G GLN* 5.0 3.3 - - + +
150Q GLY 3.4 16.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 93 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G GLN* 5.4 2.9 - - + +
92G VAL* 1.3 75.0 - - - +
94G LYS* 1.3 84.0 + - - +
95G VAL* 2.9 13.0 + - - +
96G GLY 3.1 20.3 + - - +
98G PHE* 5.5 3.8 - - + -
119G PHE* 4.0 9.1 - - - -
128G TYR* 2.9 25.1 + - - -
150Q GLY 4.2 6.5 - - - +
151Q THR* 3.1 23.9 - - - +
152Q PHE* 3.2 57.1 - - + +
161Q VAL 5.8 0.8 + - - -
----------------------------------------------------------
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