Contacts of the helix formed by residues 97 - 105 (chain B) in PDB entry 4SBV
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 97 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLU* 3.6 23.7 + - - -
74B LEU 4.2 7.0 - - - -
75B SER* 4.6 2.0 - - - -
93B PRO 4.6 0.8 + - - -
94B PHE 3.5 7.5 - - - +
95B THR 3.3 0.8 - - - -
96B VAL* 1.3 80.8 + - - +
98B THR* 1.3 62.0 + - - -
99B TRP 3.4 2.2 - - - -
100B LEU* 4.2 2.1 - - - +
101B ARG* 3.5 22.3 + - - +
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Residues in contact with THR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLU* 3.2 4.7 + - - +
74B LEU 5.1 1.1 + - - -
97B GLY* 1.3 71.3 - - - -
99B TRP* 1.3 63.0 + - - +
101B ARG* 3.4 18.8 + - - +
102B GLY* 3.0 21.7 + - - -
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Residues in contact with TRP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 3.6 38.8 - - + -
70B SER 5.6 0.2 - - - -
71B HIS* 3.0 43.2 + + + -
73B GLU* 2.3 36.9 + - - +
98B THR* 1.3 66.6 - - - +
100B LEU* 1.4 59.1 + - - +
101B ARG 2.8 2.0 + - - -
102B GLY* 3.0 3.0 + - - -
103B VAL* 2.6 64.6 + - + +
246B TYR* 3.7 4.5 - - - -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 4.1 15.9 - - + -
73B GLU* 3.3 8.4 + - - +
93B PRO* 3.2 43.3 - - + +
96B VAL* 4.4 5.8 - - + -
97B GLY 4.1 6.7 + - - +
99B TRP* 1.4 82.7 - - + +
101B ARG* 1.3 58.2 - - - +
103B VAL* 3.0 1.5 + - + -
104B ALA* 2.6 51.0 + - + +
112B TRP* 3.7 20.0 - - + -
246B TYR* 3.1 40.8 - - + +
248B ILE* 4.6 9.0 - - + -
250B LEU* 5.5 0.4 - - + -
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B PRO 3.7 7.7 + - - -
94B PHE* 2.3 92.2 + - + +
95B THR* 4.1 6.5 - - - +
97B GLY 3.5 22.6 + - - +
98B THR* 3.4 21.5 + - - +
99B TRP 2.8 0.6 - - - -
100B LEU* 1.3 81.9 - - - +
102B GLY* 1.3 64.8 + - - +
103B VAL 2.8 1.9 + - - -
104B ALA* 4.9 1.1 - - - -
105B GLN* 2.8 33.0 + - - +
199B PHE* 4.1 3.0 - - + -
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Residues in contact with GLY 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B THR 3.0 8.7 + - - -
99B TRP* 3.0 8.3 + - - -
101B ARG* 1.3 77.1 - - - +
103B VAL* 1.3 62.1 + - - +
105B GLN* 3.7 18.1 - - - +
106B ASN* 3.4 13.5 + - - +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 5.1 11.7 - - + -
99B TRP* 2.6 66.4 + - + +
100B LEU* 3.9 4.0 - - + +
101B ARG 2.8 1.0 + - - -
102B GLY* 1.3 73.0 - - - +
104B ALA* 1.3 60.9 + - - +
105B GLN 2.9 4.3 - - - -
106B ASN* 2.1 34.8 + - - +
107B TRP* 3.3 27.8 - - + -
250B LEU* 5.2 2.0 - - + -
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B PRO* 3.9 21.1 - - + -
100B LEU* 2.6 28.3 + - + +
103B VAL* 1.3 73.9 - - - +
105B GLN* 1.3 51.6 + - - +
107B TRP* 2.7 47.1 + - - +
110B TYR* 6.1 0.9 - - + -
199B PHE* 3.4 20.4 - - + -
250B LEU* 4.4 15.9 - - + +
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Residues in contact with GLN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B PHE* 5.4 3.7 - - - -
101B ARG* 2.8 29.3 + - - +
102B GLY* 3.7 21.9 - - - +
104B ALA* 1.3 74.3 - - - +
106B ASN* 1.3 57.8 + - - +
107B TRP 3.2 3.4 + - - -
199B PHE* 3.0 32.5 - - + -
201B THR* 5.2 6.1 - - - +
254B ILE* 4.2 1.4 - - - +
256B ALA* 3.8 40.3 - - + +
259B ASN* 3.5 22.7 + - - +
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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