Contacts of the helix formed by residues 97 - 105 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A GLU* 3.7 20.1 + - - -
74A LEU 4.1 10.8 - - - -
75A SER 5.4 1.1 - - - -
93A PRO 4.1 0.8 + - - -
94A PHE 3.2 4.8 - - - +
95A THR 3.4 0.8 - - - -
96A VAL* 1.3 79.6 - - - +
98A THR* 1.3 63.7 + - - -
99A TRP 3.2 2.9 - - - -
100A LEU* 5.2 0.6 - - - +
101A ARG* 2.8 27.1 + - - +
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Residues in contact with THR 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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73A GLU* 3.6 2.7 + - - -
74A LEU 5.1 1.0 + - - -
97A GLY* 1.3 72.8 - - - -
99A TRP* 1.3 67.5 + - - +
101A ARG* 3.5 30.1 - - - +
102A GLY* 3.5 12.1 + - - -
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Residues in contact with TRP 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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69A LEU* 3.7 24.2 - - + -
70A SER 5.7 0.7 - - - -
71A HIS* 3.1 49.4 + + + +
73A GLU* 2.9 21.2 + - + +
98A THR* 1.3 79.9 + - - +
100A LEU* 1.3 90.1 + - - +
101A ARG 3.0 0.4 - - - -
102A GLY* 2.8 14.2 + - - -
103A VAL* 3.0 39.0 + - + +
246A TYR* 3.3 5.2 - - - -
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Residues in contact with LEU 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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69A LEU* 5.1 1.1 - - + -
73A GLU* 2.8 22.0 + - - +
93A PRO* 3.5 37.5 - - + +
96A VAL* 4.7 5.6 - - + -
97A GLY 4.1 2.7 + - - +
99A TRP* 1.3 81.6 - - + +
101A ARG* 1.3 53.1 + - - +
103A VAL* 2.7 11.8 + - + -
104A ALA* 2.5 53.5 + - + +
112A TRP* 3.7 19.7 - - + -
246A TYR* 3.3 30.5 - - + +
248A ILE* 4.3 16.2 - - + -
250A LEU* 5.4 1.1 - - + -
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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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93A PRO 3.9 10.1 + - - -
94A PHE* 2.4 94.9 + - - +
95A THR* 3.6 6.1 - - - +
97A GLY 2.8 28.9 + - - +
98A THR* 3.5 31.7 - - - +
100A LEU* 1.3 79.6 - - - +
102A GLY* 1.3 63.6 + - - +
104A ALA 4.1 0.2 - - - -
105A GLN* 3.3 28.3 + - - +
199A PHE* 4.0 4.6 - - - -
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Residues in contact with GLY 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 THR 3.5 4.8 + - - -
99A TRP 2.8 12.2 + - - -
101A ARG* 1.3 82.2 - - - +
103A VAL* 1.3 60.5 - - - +
105A GLN* 3.3 22.1 + - - +
106A ASN* 3.2 17.3 - - - +
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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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69A LEU* 3.8 29.4 - - + -
99A TRP* 3.5 47.8 - - + +
100A LEU* 2.7 9.6 + - + +
102A GLY* 1.3 79.1 - - - +
104A ALA* 1.3 64.3 - - - +
105A GLN 3.2 1.8 - - - -
106A ASN* 3.2 13.5 - - - +
107A TRP* 3.2 29.8 - - + -
250A LEU* 4.5 1.1 - - + -
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Residues in contact with ALA 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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93A PRO* 3.8 22.7 - - + -
100A LEU* 2.5 36.3 + - + +
103A VAL* 1.3 70.5 - - - +
105A GLN* 1.3 62.4 + - - +
106A ASN 2.8 7.8 + - - -
107A TRP* 2.9 29.3 + - - +
110A TYR* 6.4 0.4 - - + -
199A PHE* 3.3 11.5 - - + -
248A ILE* 5.2 0.4 - - + -
250A LEU* 4.6 11.7 - - + -
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Residues in contact with GLN 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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94A PHE* 5.7 3.1 - - - -
101A ARG* 3.3 17.0 + - - +
102A GLY* 3.3 29.7 + - - +
104A ALA* 1.3 76.5 - - - +
106A ASN* 1.3 63.0 + - - +
107A TRP 3.1 1.5 + - - -
199A PHE* 2.8 25.7 - - + -
254A ILE* 3.8 3.8 - - - +
256A ALA* 3.9 29.8 - - + +
259A ASN* 3.0 28.5 + - + +
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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