Contacts of the helix formed by residues 98 - 105 (chain A) in PDB entry 3V5I
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 ALA 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A PRO 4.0 10.1 - - - +
68A GLY* 4.3 3.8 - - - -
69A GLY 5.0 2.5 - - - +
97A ALA* 1.3 73.2 - - + +
99A MET* 1.3 67.5 + - + +
101A SER* 2.8 24.4 + - - -
102A PHE* 3.0 5.3 + - - +
121A MET* 2.9 17.3 + - + -
122A ILE* 5.0 2.5 - - - +
123A HIS* 3.6 35.2 - - + +
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Residues in contact with MET 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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36A ILE* 4.1 13.7 - - + -
68A GLY* 4.2 0.2 - - - -
69A GLY 4.1 17.3 - - - +
70A SER 3.9 6.7 - - - +
71A VAL* 3.5 43.1 - - + +
74A GLY* 3.7 26.0 - - - -
75A PHE* 4.8 0.9 - - - -
98A ALA* 1.3 78.9 - - - +
100A GLY* 1.3 61.0 + - - +
102A PHE* 3.2 30.2 + - + +
103A LEU* 3.0 24.5 + - + +
150A LEU* 3.7 25.6 - - + -
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Residues in contact with GLY 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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36A ILE* 4.0 12.3 - - - +
64A ILE* 4.1 7.8 - - - +
66A SER* 4.4 13.2 - - - -
68A GLY* 3.9 4.4 - - - -
96A ALA* 4.0 7.8 - - - +
97A ALA 2.8 17.7 + - - -
99A MET* 1.3 77.9 - - - +
101A SER* 1.3 55.6 + - - -
103A LEU* 3.2 7.3 + - - +
104A LEU* 3.0 25.1 + - - +
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Residues in contact with SER 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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96A ALA* 3.4 23.4 - - - -
97A ALA 3.6 3.8 + - - -
98A ALA 2.8 18.9 + - - -
100A GLY* 1.3 69.9 - - - -
102A PHE* 1.3 65.5 + - - +
104A LEU* 3.3 10.3 + - - +
105A ALA* 3.1 23.9 + - - +
120A VAL* 3.6 21.3 - - - -
121A MET 3.3 12.1 + - - -
122A ILE* 3.3 15.7 - - - +
185A LEU* 4.5 6.4 - - - +
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Residues in contact with PHE 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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74A GLY 5.6 0.4 - - - -
75A PHE* 3.6 32.8 - + - -
78A TYR* 3.6 25.5 - + + -
98A ALA 3.0 7.0 + - - +
99A MET* 3.3 37.7 - - + +
100A GLY 3.1 0.2 - - - -
101A SER* 1.3 80.1 + - - +
103A LEU* 1.3 66.5 + - + +
105A ALA* 3.2 4.9 + - - +
106A ALA* 3.2 18.9 + - - +
150A LEU* 3.7 37.7 - - + -
153A ILE* 3.8 25.1 - - + -
154A LEU* 4.0 27.3 - - + +
157A ARG* 5.8 1.0 - - - -
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Residues in contact with LEU 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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32A LEU* 4.2 12.3 - - + -
36A ILE* 3.9 26.2 - - + -
62A LEU* 5.4 2.2 - - + -
64A ILE* 4.0 11.0 - - + -
74A GLY* 3.5 25.8 - - - +
77A ILE* 3.9 31.4 - - + -
78A TYR* 3.8 25.4 - - + +
81A ILE* 4.8 8.1 - - + +
90A THR* 3.7 7.8 - - - +
99A MET* 3.0 15.0 + - + +
100A GLY* 3.2 6.7 + - - +
102A PHE* 1.3 78.2 - - + +
104A LEU* 1.3 66.7 + - - +
106A ALA* 2.9 18.0 + - - +
107A GLY 3.6 3.6 + - - -
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Residues in contact with LEU 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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64A ILE* 3.6 12.7 - - + +
90A THR* 2.7 36.1 + - - +
91A ILE 4.4 0.2 - - - +
92A CYS* 3.7 31.6 - - + +
96A ALA* 4.1 7.9 - - + -
100A GLY 3.0 13.7 + - - +
101A SER* 3.3 11.9 + - - +
103A LEU* 1.3 74.9 - - - +
105A ALA* 1.3 61.2 + - - +
106A ALA 3.2 1.2 + - - -
107A GLY 3.5 1.9 + - - -
112A ARG* 3.6 6.4 - - - +
113A PHE 3.5 23.6 - - - +
114A ALA* 5.4 0.2 - - + -
120A VAL* 3.9 24.2 - - + -
185A LEU* 4.4 4.5 - - + +
186A ILE* 3.7 23.8 - - + -
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Residues in contact with ALA 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 SER 3.1 13.4 + - - +
102A PHE 3.6 5.8 - - - +
103A LEU 3.2 0.2 - - - -
104A LEU* 1.3 77.7 - - - +
106A ALA* 1.3 57.2 + - - +
107A GLY 3.4 0.7 - - - -
112A ARG* 2.8 27.8 + - - +
154A LEU* 4.3 12.1 - - + -
157A ARG* 3.6 17.6 + - + -
158A THR* 5.0 1.3 - - + -
185A LEU* 3.3 41.7 - - + +
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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