Contacts of the strand formed by residues 119 - 125 (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 PHE 119 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114F ILE* 3.2 8.6 - - - +
115F HIS* 2.9 54.8 + + + +
116F ASP* 4.2 22.9 - - + -
117F VAL 3.4 2.2 + - - -
118F ASP* 1.3 86.2 - - + +
120F LEU* 1.3 59.9 - - - +
166F ARG* 4.1 21.1 - - + -
167F PHE 3.6 5.8 - - - +
168F ASP* 3.1 48.5 - - + -
170F ILE* 4.3 1.3 - - - -
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Residues in contact with LEU 120 (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* 4.3 5.6 - - + -
113F TRP 3.3 34.1 - - - +
114F ILE* 3.7 12.3 - - + +
119F PHE* 1.3 72.3 - - - +
121F SER* 1.3 71.2 + - - +
122F CYS* 4.9 2.5 - - - -
140F LEU* 3.6 31.6 - - + -
166F ARG* 3.3 2.1 - - - +
167F PHE* 2.8 43.4 + - + +
170F ILE* 3.6 31.8 - - + +
182F ILE* 4.5 10.3 - - + -
202F PHE* 4.3 11.0 - - + -
205F ILE* 4.2 8.7 - - + -
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Residues in contact with SER 121 (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* 3.2 0.9 - - - -
113F TRP* 2.9 55.7 + - - -
115F HIS* 2.3 39.5 + - - -
120F LEU* 1.3 78.4 + - - +
122F CYS* 1.3 64.0 + - - +
165F CYS 3.3 10.8 - - - -
166F ARG* 3.2 11.0 - - - +
167F PHE* 5.9 0.2 - - - -
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Residues in contact with CYS 122 (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* 5.3 0.9 - - + -
111F THR 3.4 4.3 - - - -
112F CYS* 2.0 47.1 - - - -
113F TRP* 4.0 2.7 - - - -
120F LEU* 4.9 6.3 - - - -
121F SER* 1.3 74.9 - - - +
123F SER* 1.3 62.2 + - - +
124F TRP* 4.2 4.9 - - + -
138F LEU* 3.7 33.2 - - + -
164F GLY* 3.3 1.7 - - - -
165F CYS* 2.9 35.1 + - + +
167F PHE* 5.3 4.7 - - - -
182F ILE* 3.8 11.9 - - - -
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Residues in contact with SER 123 (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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109F ASN 3.2 4.7 - - - +
111F THR* 2.9 42.0 + - - +
113F TRP* 3.7 19.4 - - - -
122F CYS* 1.3 77.2 - - - +
124F TRP* 1.3 63.9 + - - +
155F LYS* 6.5 0.9 - - - -
163F ILE* 3.8 8.1 - - - -
164F GLY* 4.8 2.5 - - - -
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Residues in contact with TRP 124 (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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107F ALA* 3.4 26.2 - - + -
108F GLU 3.4 12.8 - - - +
109F ASN* 3.6 5.4 - - - -
110F LEU* 3.9 20.4 - - + -
122F CYS* 4.1 3.4 - - + -
123F SER* 1.3 82.5 - - - +
125F ALA* 1.3 67.7 + - - +
126F VAL 4.5 0.4 - - - -
136F TYR* 3.7 26.7 - + + -
138F LEU* 3.5 37.0 - - + -
154F TYR* 4.4 5.4 - + - -
162F ARG* 2.9 36.1 + - + -
163F ILE* 3.0 38.3 + - - +
164F GLY* 3.2 31.2 - - - -
165F CYS* 4.0 3.6 - - + -
184F VAL* 4.4 12.1 - - + -
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Residues in contact with ALA 125 (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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107F ALA* 3.5 3.5 - - - -
108F GLU* 2.7 43.6 + - + +
109F ASN* 4.5 11.2 - - + -
124F TRP* 1.3 79.0 - - - +
126F VAL* 1.3 67.3 + - + +
127F GLY 3.4 0.5 + - - -
163F ILE* 4.7 5.4 - - + -
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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