Contacts of the helix formed by residues 92 - 105 (chain A) in PDB entry 1NMS
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 THR 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A HIS* 4.5 11.9 - - + +
90A ASP 5.4 0.9 - - - +
91A LEU* 1.3 76.3 - - - +
93A ARG* 1.3 65.3 + - - +
94A GLU* 3.6 13.5 + - - +
95A GLU* 2.9 38.0 + - - +
96A ILE* 2.9 20.3 + - - +
129A GLY* 3.9 0.4 - - - -
130A THR* 3.4 16.2 - - - +
131A ASN* 3.3 19.7 - - - +
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Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A THR* 1.3 72.1 - - - +
94A GLU* 1.3 85.7 + - - +
96A ILE* 3.3 7.8 + - - +
97A VAL* 3.0 28.3 + - - +
129A GLY* 3.6 7.9 - - - -
131A ASN* 2.8 25.9 + - - +
132A GLY* 3.7 21.9 - - - +
133A PRO* 3.1 45.8 + - - +
134A VAL* 4.1 17.9 - - + +
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A THR* 3.2 9.8 + - - +
93A ARG* 1.3 102.3 + - + +
95A GLU* 1.3 57.6 + - + +
97A VAL* 3.4 6.8 + - - +
98A GLU* 3.0 28.6 + - - +
131A ASN* 2.9 24.9 + - - -
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ASP 4.0 3.8 - - - +
91A LEU* 3.4 26.9 - - + +
92A THR* 2.9 46.0 + - - +
94A GLU* 1.3 75.2 - - + +
96A ILE* 1.3 61.4 + - - +
98A GLU* 3.8 17.1 - - - +
99A LEU* 2.8 31.9 + - - +
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 4.0 27.8 - - + -
52A ASN* 4.0 12.3 - - - +
91A LEU* 3.8 17.7 - - + -
92A THR 2.9 12.7 + - - +
93A ARG* 3.3 9.8 + - - +
95A GLU* 1.3 77.8 - - - +
97A VAL* 1.3 64.8 + - + +
99A LEU* 3.5 2.5 - - - +
100A MET* 3.0 25.1 + - + +
118A LEU* 5.4 1.6 - - + -
127A ILE* 5.1 7.6 - - + -
128A PHE 4.3 2.7 - - - +
129A GLY* 3.8 31.6 - - - +
134A VAL* 4.7 8.7 - - + -
139A ILE* 3.7 32.3 - - + -
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ARG 3.0 21.2 + - - +
94A GLU* 3.8 5.4 - - - +
96A ILE* 1.3 78.9 - - + +
98A GLU* 1.3 57.5 + - - +
100A MET* 3.4 4.3 + - - -
101A ARG* 2.9 43.8 + - - +
134A VAL* 4.0 16.2 - - + -
138A LYS* 3.8 42.6 - - + +
139A ILE* 5.1 4.3 - - + -
142A PHE* 3.7 24.5 - - + -
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Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLU 3.0 17.5 + - - +
95A GLU* 3.9 19.4 - - - +
97A VAL* 1.3 75.1 - - - +
99A LEU* 1.3 61.1 + - - +
101A ARG* 3.5 12.8 + - - +
102A ASP* 2.9 51.5 + - - +
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ILE* 3.9 26.5 - - + -
50A ILE* 4.0 5.8 - - + -
86A ARG* 6.1 1.1 - - - +
88A LYS* 3.9 41.3 - - + +
91A LEU* 3.9 15.9 - - + -
95A GLU 2.8 19.0 + - - +
96A ILE 3.5 3.4 - - - +
98A GLU* 1.3 79.7 - - - +
100A MET* 1.3 68.6 + - + +
102A ASP* 3.2 7.6 + - + +
103A VAL* 2.9 43.9 + - + +
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Residues in contact with MET 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ILE* 4.1 17.7 - - + -
50A ILE* 4.1 13.0 - - + -
96A ILE* 3.0 22.7 + - + +
97A VAL* 3.8 3.8 - - - +
99A LEU* 1.3 97.3 - - + +
101A ARG* 1.3 66.3 + - - +
103A VAL* 3.4 4.4 + - + -
104A SER* 2.9 26.2 + - - -
114A PHE* 5.1 2.0 - - + -
116A CYS* 4.0 17.3 - - + -
139A ILE* 3.6 37.2 - - + +
142A PHE* 3.9 18.2 - - + -
143A PHE* 3.7 22.9 - - + -
158A PHE* 5.0 0.2 - - - -
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Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A VAL* 2.9 39.6 + - - +
98A GLU* 3.7 11.5 - - - +
100A MET* 1.3 76.5 - - - +
102A ASP* 1.3 69.3 + - - +
104A SER* 2.7 22.6 + - - +
105A LYS* 3.2 39.3 + - + +
138A LYS* 5.9 0.4 - - - +
142A PHE* 3.6 31.9 - - + -
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Residues in contact with ASP 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLU* 2.9 36.9 + - - +
99A LEU* 3.7 7.7 - - + +
101A ARG* 1.3 84.8 - - - +
103A VAL* 1.3 64.7 + - + +
105A LYS* 3.1 19.7 + - - +
106A GLU* 3.3 14.7 + - - +
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Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.9 13.2 - - + -
48A ILE* 4.3 12.3 - - + -
86A ARG* 4.2 18.6 - - - +
99A LEU* 2.9 38.5 + - + +
100A MET* 3.9 7.0 - - + +
102A ASP* 1.3 76.3 - - + +
104A SER* 1.3 60.3 + - - +
106A GLU* 3.2 16.5 + - - +
108A HIS* 2.8 24.9 + - + -
114A PHE* 3.6 36.3 - - + -
143A PHE* 4.1 5.4 - - + -
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Residues in contact with SER 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A MET 2.9 15.4 + - - -
101A ARG* 2.7 18.5 + - - -
102A ASP 3.2 0.2 - - - -
103A VAL* 1.3 77.7 - - - +
105A LYS* 1.3 63.6 + - - +
106A GLU 3.4 2.9 + - - +
142A PHE* 3.4 40.4 + - - +
143A PHE* 3.7 18.6 - - - -
147A ARG 4.7 4.0 + - - +
148A CYS* 3.3 26.9 - - - +
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Residues in contact with LYS 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ARG* 3.2 43.4 + - + +
102A ASP* 3.1 13.8 + - - +
104A SER* 1.3 81.8 - - - +
106A GLU* 1.3 63.8 + - - +
147A ARG 6.1 1.3 - - - +
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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