Contacts of the helix formed by residues 90 - 100 (chain A) in PDB entry 2DVL
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 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A SER 2.8 19.2 + - - -
87A VAL* 3.0 7.3 + - - -
88A THR 3.3 0.4 - - - -
89A SER* 1.3 81.2 - - - +
91A LEU* 1.3 66.1 + - - -
92A PRO 3.3 1.3 - - - -
93A GLN 3.1 3.3 + - - -
94A TYR* 2.9 23.9 + - - +
235A GLY* 6.3 3.6 - - - -
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Residues in contact with LEU 91 (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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87A VAL 4.3 0.2 + - - -
90A GLY* 1.3 69.7 - - - -
92A PRO* 1.3 70.9 - - + +
94A TYR* 4.0 3.6 - - + -
95A MET* 2.8 37.7 + - + +
121A PHE* 3.3 52.3 - - + -
228A ALA* 3.4 31.6 - - + +
231A GLY* 3.4 30.3 - - - +
232A LEU* 5.4 9.9 - - + +
356A GLU* 5.8 4.3 - - - +
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Residues in contact with PRO 92 (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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87A VAL* 3.2 23.1 - - + +
88A THR 4.1 9.6 - - - +
90A GLY 3.3 1.6 - - - -
91A LEU* 1.3 94.6 - - + +
93A GLN* 1.3 59.2 + - - +
95A MET* 4.4 1.0 - - - +
96A LEU* 3.3 31.7 + - - +
112A LEU* 4.6 11.2 - - + -
119A GLY* 4.3 2.5 - - - -
120A ALA 3.8 36.6 - - - +
121A PHE* 4.1 7.9 - - + +
163A LEU* 5.8 1.6 - - + +
165A VAL* 4.1 20.4 - - + +
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Residues in contact with GLN 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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49A LEU 3.0 23.4 + - - -
50A GLY* 4.0 5.2 - - - -
52A THR* 4.4 3.6 + - - +
53A THR* 2.7 28.9 + - - +
88A THR* 3.0 25.0 + - - +
89A SER* 3.2 14.2 - - - +
90A GLY 3.1 6.2 + - - +
92A PRO* 1.3 76.3 - - - +
94A TYR* 1.3 66.9 + - - +
95A MET 3.3 0.2 - - - -
96A LEU 4.6 0.2 - - - +
97A LEU* 3.0 27.5 + - - +
109A LEU* 3.8 20.0 - - + +
112A LEU* 3.7 25.6 + - + +
113A ALA* 3.7 18.8 - - - +
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Residues in contact with TYR 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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52A THR* 5.6 0.6 + - - -
89A SER 5.0 0.6 + - - +
90A GLY 2.9 18.6 + - - +
91A LEU* 3.8 9.2 - - + +
93A GLN* 1.3 78.4 - - - +
95A MET* 1.3 62.8 + - + +
97A LEU* 3.7 6.7 - - + +
98A ARG* 2.5 74.9 + - + +
99A PHE* 4.5 3.1 - + - -
227A TYR 4.5 4.9 - - - -
230A ALA* 3.3 23.0 + - + -
231A GLY* 3.5 32.5 - - - -
234A SER* 4.0 21.3 + - - -
299A LYS* 4.7 7.4 - - - -
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Residues in contact with MET 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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91A LEU* 2.8 29.4 + - + +
92A PRO* 4.4 2.0 - - + +
94A TYR* 1.3 76.8 - - + +
96A LEU* 1.3 60.2 + - - +
99A PHE* 2.9 40.9 + - + +
100A GLY 3.5 0.9 + - - -
121A PHE* 3.7 25.6 - - - -
165A VAL* 4.0 13.2 - - + -
167A MET* 4.3 7.6 - - - -
176A ALA* 3.6 31.6 - - + -
218A LEU* 3.7 18.1 - - + +
224A GLY 4.5 0.2 - - - +
227A TYR* 3.9 33.9 - - + +
228A ALA* 4.3 9.0 - - - +
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Residues in contact with LEU 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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92A PRO 3.3 19.8 + - - +
93A GLN 3.5 3.7 + - - +
94A TYR 3.4 0.4 - - - -
95A MET* 1.3 75.0 - - - +
97A LEU* 1.3 64.4 + - - +
100A GLY* 2.7 29.5 + - - +
104A GLN* 4.4 15.5 - - + +
105A LYS* 3.5 8.8 - - + +
108A TYR* 3.7 26.7 - - + -
109A LEU* 3.8 24.0 - - + +
112A LEU* 4.0 14.4 - - + -
163A LEU* 4.2 5.4 - - + -
165A VAL* 5.6 1.1 - - + -
178A LEU* 3.9 33.4 - - + -
218A LEU* 4.1 14.8 - - + -
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Residues in contact with LEU 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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52A THR 4.6 9.9 - - - +
53A THR* 4.7 2.5 - - + +
54A PRO* 3.8 29.8 - - + -
57A TRP* 3.6 33.2 - - + +
93A GLN 3.0 19.1 + - - +
94A TYR* 3.7 6.1 - - + +
96A LEU* 1.3 80.7 - - - +
98A ARG* 1.3 69.3 + - + +
100A GLY 4.3 1.4 + - - +
105A LYS* 3.7 18.0 + - + +
109A LEU* 3.7 17.1 - - + +
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Residues in contact with ARG 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 TYR* 2.5 67.1 + - + +
97A LEU* 1.3 91.5 - - + +
99A PHE* 1.3 94.7 + - + +
100A GLY 5.2 0.4 - - - +
230A ALA* 4.3 9.1 + - - +
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Residues in contact with PHE 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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94A TYR* 4.5 2.9 - + - -
95A MET* 2.9 28.8 + - + +
98A ARG* 1.3 121.8 - - + +
100A GLY* 1.3 68.4 + - - +
104A GLN* 4.6 0.2 - - - +
218A LEU* 3.8 13.5 - - + +
219A GLY* 4.0 12.3 + - - -
227A TYR* 3.4 76.9 - + + -
230A ALA* 4.3 8.7 - - + -
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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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95A MET 3.5 2.2 + - - -
96A LEU* 2.7 26.8 + - - -
97A LEU 4.7 1.0 - - - +
98A ARG 5.2 0.5 - - - -
99A PHE* 1.3 77.5 - - - +
101A SER* 1.3 66.3 + - - -
104A GLN* 3.3 6.1 - - - -
105A LYS* 3.7 14.8 + - - -
218A LEU* 3.3 18.6 - - - +
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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