Contacts of the helix formed by residues 98 - 107 (chain A) in PDB entry 1SNG
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 ARG 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ARG* 4.9 0.7 - - - -
97A VAL* 1.3 74.9 - - - +
99A SER* 1.3 65.7 + - - +
100A SER* 3.8 11.3 + - - +
101A PHE* 3.1 5.5 + - - +
102A ARG* 3.1 18.8 + - - +
287A SER* 3.1 29.1 + - - -
288A GLY* 3.5 22.6 - - - +
289A ILE 2.8 18.8 + - - +
290A SER* 4.4 3.8 - - - +
291A THR* 4.4 21.8 - - + +
501A SO4 3.0 37.5 + - - +
502A SO4 3.5 42.8 + - - -
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Residues in contact with SER 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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97A VAL 3.6 3.3 + - - -
98A ARG* 1.3 71.4 - - - +
100A SER* 1.3 58.4 + - - +
102A ARG* 3.3 14.5 + - - +
103A ALA* 2.9 28.6 + - - +
501A SO4 3.2 13.3 + - - -
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Residues in contact with SER 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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98A ARG* 3.8 14.6 + - - +
99A SER* 1.3 76.2 - - - +
101A PHE* 1.3 58.8 + - - +
103A ALA* 3.4 8.8 + - - +
104A THR* 3.1 29.0 + - - -
288A GLY 4.4 2.8 + - - -
501A SO4 2.8 33.2 + - - -
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Residues in contact with PHE 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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45A VAL* 3.4 44.4 - - + -
46A LEU* 4.5 4.9 - - + -
48A ALA 5.2 0.7 - - - -
49A GLY* 4.1 11.7 - - - -
89A LEU* 3.6 28.9 - - + -
97A VAL* 3.9 9.9 - - + -
98A ARG 3.1 9.2 + - - +
100A SER* 1.3 79.1 + - - +
102A ARG* 1.3 67.3 + - - +
104A THR* 3.2 10.6 + - - -
105A MET* 3.0 23.0 + - + +
113A VAL* 4.0 13.9 - - + -
288A GLY 3.4 16.8 - - - +
289A ILE* 3.7 46.2 - - + +
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Residues in contact with ARG 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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97A VAL* 3.4 46.1 + - + +
98A ARG 3.1 13.6 + - - +
99A SER* 3.3 16.6 + - - +
101A PHE* 1.3 76.7 - - - +
103A ALA* 1.3 58.3 + - - +
105A MET* 3.4 2.6 + - - +
106A HIS* 2.9 29.3 + - - +
112A ASP* 5.7 0.8 + - - -
113A VAL* 3.9 41.0 + - + +
114A ARG* 5.3 1.6 - - - +
115A THR* 4.6 13.5 + - - -
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Residues in contact with ALA 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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99A SER 2.9 13.0 + - - +
100A SER* 3.5 12.8 - - - +
101A PHE 3.1 0.4 - - - -
102A ARG* 1.3 74.5 - - - +
104A THR* 1.3 65.5 + - - +
106A HIS* 3.1 7.8 + - - +
107A ASP* 2.9 36.2 + - - +
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Residues in contact with THR 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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45A VAL* 4.3 14.1 - - + +
48A ALA* 4.0 27.9 - - + +
70A LEU* 4.4 7.2 - - + -
100A SER 3.1 16.3 + - - -
101A PHE* 3.2 13.9 + - - -
103A ALA* 1.3 74.9 - - - +
105A MET* 1.3 62.9 + - - +
107A ASP* 3.5 9.2 + - - -
108A ARG* 2.9 38.6 + - - +
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Residues in contact with MET 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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41A CAF 4.8 1.8 - - - +
45A VAL* 3.8 32.3 - - + +
87A THR* 4.4 15.9 - - + -
89A LEU* 3.9 30.3 - - + +
101A PHE* 3.0 18.1 + - + +
102A ARG 3.7 7.2 - - - +
104A THR* 1.3 76.4 - - - +
106A HIS* 1.3 63.0 + - - +
108A ARG* 3.1 23.2 + - - +
111A SER* 3.5 23.7 - - - -
112A ASP* 3.6 34.1 - - - +
113A VAL* 3.9 12.1 - - + +
158A LEU* 4.8 7.6 - - + -
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Residues in contact with HIS 106 (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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102A ARG 2.9 18.5 + - - +
103A ALA* 3.1 8.0 + - - +
105A MET* 1.3 76.6 - - - +
107A ASP* 1.3 69.9 + - - +
108A ARG 3.1 9.8 - - - +
111A SER 4.2 11.8 + - - +
112A ASP* 5.9 0.2 - - - +
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Residues in contact with ASP 107 (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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74A ASP* 3.6 14.0 - - - +
103A ALA* 2.9 26.0 + - - +
104A THR* 3.7 9.0 - - - +
105A MET 3.2 0.4 - - - -
106A HIS* 1.3 85.4 - - - +
108A ARG* 1.3 79.7 + - - +
109A PRO* 4.1 0.5 - - - +
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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