Contacts of the helix formed by residues 120 - 128 (chain F) in PDB entry 2NYM
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 SER 120 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117F ASN 3.8 4.3 + - - -
118F HIS 2.6 10.0 + - - +
119F GLU* 1.3 76.2 - - - +
121F ARG* 1.3 66.4 + - - +
122F GLN 4.1 0.5 + - - -
123F ILE* 3.2 26.9 + - - +
124F THR* 3.1 22.7 + - - +
147F THR 6.1 0.2 - - - -
150F PHE* 4.8 2.5 - - - -
188F GLU* 3.0 25.5 + - - -
189F VAL* 3.7 22.6 - - - +
5H 1ZN 4.7 4.7 - - - -
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Residues in contact with ARG 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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372E TRP* 3.6 50.3 - - + +
120F SER* 1.3 71.2 - - - +
122F GLN* 1.3 66.4 + - - +
123F ILE 2.9 1.4 + - - -
124F THR* 3.1 4.3 + - - -
125F GLN* 2.9 23.3 + - - +
143F TRP* 3.7 22.4 - - + -
147F THR* 3.8 30.5 + - - +
148F ASP* 3.2 23.2 + - - -
151F ASP* 2.9 34.6 + - - -
188F GLU* 2.5 50.5 + - - +
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Residues in contact with GLN 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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330E PHE* 3.7 31.3 - - + -
372E TRP* 3.9 18.5 - - + -
373E ASN* 5.7 1.2 - - - +
120F SER 3.5 0.2 - - - -
121F ARG* 1.3 78.1 - - - +
123F ILE* 1.3 66.8 + - + +
125F GLN* 3.5 3.2 + - - +
126F VAL* 3.2 22.0 + - + +
188F GLU* 3.4 7.7 + - - +
191F HIS* 3.2 28.4 + - - -
5H 1ZN 3.9 37.5 + - + +
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Residues in contact with ILE 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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88F ASP* 3.5 3.4 - - - +
117F ASN 3.7 7.6 - - - +
118F HIS* 2.9 42.0 - - + +
120F SER* 3.2 21.6 + - - +
121F ARG 2.9 1.6 + - - -
122F GLN* 1.3 76.5 - - + +
124F THR* 1.3 59.8 + - - +
125F GLN 2.8 1.1 - - - -
126F VAL* 2.5 28.8 + - - -
127F TYR* 2.8 36.0 + - + -
200F TRP* 3.7 24.9 - - + -
5H 1ZN 3.7 33.4 - - + -
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Residues in contact with THR 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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87F VAL* 4.2 4.3 - - + -
88F ASP* 3.4 16.6 - - - +
118F HIS 3.1 18.4 - - - +
120F SER 3.1 18.5 + - - +
121F ARG* 3.1 7.0 + - - +
123F ILE* 1.3 76.3 - - - +
125F GLN* 1.3 62.1 + - - +
128F GLY 3.1 18.0 + - - -
129F PHE* 3.6 28.3 - - + -
130F TYR* 3.2 13.3 + - - +
143F TRP* 2.8 27.5 + - - +
147F THR* 5.3 0.2 - - + -
150F PHE* 4.3 7.4 - - + -
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Residues in contact with GLN 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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289E PRO* 5.8 0.7 - - - +
328E PRO 2.9 14.5 + - - -
329E HIS* 2.9 42.0 - - + +
330E PHE* 2.9 39.2 + - + -
372E TRP* 2.9 31.9 - - - -
121F ARG 2.9 13.3 + - - +
122F GLN 3.6 6.5 - - - +
123F ILE 2.6 5.3 + - - -
124F THR* 1.3 76.8 + - - +
126F VAL* 1.3 61.1 + - - +
128F GLY 4.6 1.2 + - - -
130F TYR* 3.8 21.8 - - + +
131F ASP* 4.8 5.2 - - - +
143F TRP* 3.1 23.3 - - + -
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Residues in contact with VAL 126 (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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289E PRO* 5.3 8.5 - - - +
330E PHE* 3.9 23.3 - - + -
331E GLN* 4.5 19.6 - - - +
122F GLN* 3.2 18.1 + - + +
123F ILE* 2.5 15.1 + - - +
125F GLN* 1.3 76.0 - - - +
127F TYR* 1.3 93.3 + - + +
128F GLY 3.6 0.5 + - - -
131F ASP* 5.4 2.1 - - - +
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Residues in contact with TYR 127 (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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88F ASP* 2.9 27.1 - - + +
89F ARG* 3.3 48.9 + - - +
118F HIS* 3.9 7.4 - + + -
123F ILE* 2.8 39.0 + - + +
126F VAL* 1.3 94.3 - - + +
128F GLY* 1.3 54.7 + - - +
3H ACB 3.0 26.5 + - - -
5H 1ZN 3.1 45.5 - - + +
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Residues in contact with GLY 128 (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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88F ASP* 2.9 6.1 + - - -
89F ARG 5.3 0.9 - - - -
93F SER* 5.4 0.9 - - - -
124F THR 3.1 7.0 + - - -
125F GLN 4.6 1.2 + - - -
126F VAL 3.5 3.2 + - - -
127F TYR* 1.3 79.9 - - - +
129F PHE* 1.3 64.5 + - - -
130F TYR 3.0 4.1 + - - -
131F ASP* 3.1 13.8 + - - +
132F GLU* 2.9 25.7 + - - +
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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