Contacts of the strand formed by residues 192 - 201 (chain F) in PDB entry 6NMY
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 192 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101F GLY* 3.2 26.6 - - - -
102F LYS 3.3 6.9 + - - -
188F SER 5.8 0.2 - - - -
191F PHE* 1.3 72.8 - - - +
193F ILE* 1.3 63.0 + - - +
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Residues in contact with ILE 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F GLY* 4.9 0.7 - - - -
102F LYS* 4.6 1.6 - - + -
105F ALA* 3.4 41.1 - - + +
106F GLY* 3.7 2.0 - - - +
131F PRO* 4.6 4.5 - - + -
134F VAL* 3.8 22.9 - - + -
136F TYR* 4.5 3.6 - - + -
185F ARG* 5.4 1.2 - - - +
186F GLY* 3.7 42.7 + - - +
187F ARG 4.1 1.1 - - - +
188F SER* 3.9 24.9 - - - +
191F PHE* 4.2 11.2 - - + -
192F GLY* 1.3 76.4 - - - +
194F PRO* 1.3 77.7 - - + +
195F CYS* 3.9 0.5 + - - +
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Residues in contact with PRO 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F CYS 5.9 1.8 - - - +
100F SER 3.8 19.5 - - - +
101F GLY* 3.9 12.1 - - - -
102F LYS 3.5 25.1 - - - +
103F PRO* 5.4 1.8 - - + -
104F TRP 5.5 1.3 - - - +
105F ALA 4.9 0.7 - - - +
106F GLY* 3.3 32.5 - - - +
107F ALA 4.6 0.2 + - - -
136F TYR* 5.3 0.5 - - - -
184F VAL 4.7 0.2 - - - +
186F GLY 4.3 3.7 + - - -
192F GLY 3.9 0.2 - - - +
193F ILE* 1.3 97.8 - - + +
195F CYS* 1.3 64.2 + - - +
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Residues in contact with CYS 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F LEU* 3.7 10.8 - - - -
76F CYS* 2.0 54.7 - - - +
106F GLY* 4.9 1.4 - - - -
183F LEU* 3.6 12.6 - - + -
184F VAL 3.2 15.7 - - - +
185F ARG* 3.8 23.1 - - + +
193F ILE 3.9 0.8 + - - +
194F PRO* 1.3 79.2 - - - +
196F THR* 1.3 69.5 + - - +
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Residues in contact with THR 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F CYS* 3.7 6.1 - - - -
106F GLY 4.1 0.7 - - - -
107F ALA* 2.5 42.6 + - - +
108F GLU* 4.9 3.1 - - + -
109F ASN 5.7 0.2 - - - +
110F LEU* 4.3 23.1 - - + +
183F LEU 3.6 0.7 - - - -
184F VAL* 2.9 36.5 + - - +
195F CYS* 1.3 82.8 + - - +
197F ASP* 1.3 67.5 + - - +
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Residues in contact with ASP 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F SER* 2.9 26.4 + - - -
75F LEU 2.9 25.3 + - - -
76F CYS* 3.4 19.6 - - - +
77F GLU* 4.4 1.2 + - - +
110F LEU* 5.0 2.0 - - - +
181F HIS* 3.3 25.3 + - + -
182F ILE 3.2 13.0 - - - +
183F LEU* 4.1 3.1 - - - -
196F THR* 1.3 82.9 - - - +
198F LYS* 1.3 65.4 + - - +
199F PHE* 4.2 4.1 - - - -
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Residues in contact with LYS 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F LEU* 2.7 49.1 + - + +
111F THR* 3.7 19.1 - - - +
112F CYS 4.9 3.3 - - - +
181F HIS* 3.8 1.7 - - - -
182F ILE* 2.9 35.1 + - + +
197F ASP* 1.3 77.6 - - - +
199F PHE* 1.3 78.9 + - - +
200F VAL* 3.8 19.9 + - + +
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Residues in contact with PHE 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F GLN* 4.4 7.2 - - - -
71F GLY 4.5 3.4 - - - -
72F ALA* 3.4 46.7 - - + -
73F ILE 3.2 28.9 - - - -
74F SER* 4.0 11.4 - - - -
145F ARG* 5.5 1.3 - - + -
180F SER 3.6 5.8 - - - +
181F HIS* 3.2 36.3 - + + -
197F ASP* 4.2 4.3 - - - -
198F LYS* 1.3 85.1 - - - +
200F VAL* 1.3 61.0 + - - +
201F VAL* 5.8 0.2 - - - -
42J GLY* 6.0 4.3 - - - -
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Residues in contact with VAL 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F CYS* 4.6 6.3 - - + +
179F SER* 3.3 6.4 - - - -
180F SER* 2.9 53.6 + - - +
182F ILE* 3.9 28.0 - - + -
198F LYS* 3.8 24.0 - - + +
199F PHE* 1.3 79.2 - - - +
201F VAL* 1.3 63.3 + - - +
202F PHE* 4.0 6.7 - - + -
205F ILE* 4.1 31.6 - - + -
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Residues in contact with VAL 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178F GLN* 3.5 18.6 - - + +
179F SER* 4.4 2.9 - - - -
199F PHE 5.8 0.7 - - - +
200F VAL* 1.3 78.7 - - - +
202F PHE* 1.3 68.3 + - - +
203F SER* 4.2 12.6 - - - +
204F GLN* 2.8 39.0 + - + +
205F ILE* 3.5 10.8 + - - +
45J GLN* 3.4 25.6 - - - +
49J MET* 3.9 22.0 - - + -
113J PHE* 4.2 15.7 - - + -
117J THR* 5.3 3.6 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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