Contacts of the helix formed by residues 92 - 107 (chain A) in PDB entry 3EDY
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 SER 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ARG 4.6 0.4 + - - -
56A GLN* 3.2 26.5 + - - +
91A PRO* 1.3 76.9 - - - +
93A PRO* 1.3 75.5 - - - +
94A LEU* 3.5 9.7 + - - +
95A THR* 3.0 28.1 + - - -
96A LEU* 3.0 21.5 + - - +
166A HIS* 5.6 0.3 - - - -
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Residues in contact with PRO 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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56A GLN* 5.0 1.6 - - - +
91A PRO 4.3 2.5 - - - +
92A SER* 1.3 86.0 - - - +
94A LEU* 1.3 61.8 + - - +
96A LEU* 3.4 9.7 + - + +
97A HIS* 2.9 49.3 + - + +
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Residues in contact with LEU 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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92A SER* 3.2 9.8 + - - +
93A PRO* 1.3 79.1 - - - +
95A THR* 1.3 61.7 + - - +
97A HIS* 4.7 4.7 - - + -
98A THR* 2.6 51.5 + - - +
166A HIS* 4.0 18.6 - - + +
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Residues in contact with THR 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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53A LEU* 4.2 7.2 - - + -
54A ARG* 4.1 10.6 + - - +
91A PRO* 3.7 22.4 - - + -
92A SER* 3.0 22.6 + - - -
94A LEU* 1.3 76.3 - - - +
96A LEU* 1.3 64.3 + - - +
98A THR* 3.8 0.3 - - - -
99A VAL* 3.0 31.5 + - + +
165A PRO 4.0 7.8 + - - -
166A HIS* 3.1 49.0 + - + +
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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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53A LEU* 3.9 14.6 - - + -
90A ARG* 5.4 1.3 - - - -
91A PRO* 3.9 27.1 - - + +
92A SER 3.0 16.9 + - - +
93A PRO* 3.9 7.2 - - + +
95A THR* 1.3 75.8 - - - +
97A HIS* 1.3 63.7 + - + +
99A VAL* 4.0 3.1 - - - +
100A GLN* 2.9 53.1 + - + +
117A GLN* 3.6 49.6 - - + +
120A LEU* 6.5 0.2 - - + -
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Residues in contact with HIS 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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93A PRO* 2.9 38.1 + - + +
94A LEU* 4.0 5.8 - - + +
96A LEU* 1.3 78.5 - - + +
98A THR* 1.3 60.9 + - - +
100A GLN* 3.7 16.8 - - - +
101A LYS* 3.0 59.5 + - - +
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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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94A LEU* 2.6 41.2 + - - +
95A THR* 3.8 4.3 - - - -
97A HIS* 1.3 78.0 - - - +
99A VAL* 1.3 61.2 + - - +
101A LYS* 4.0 6.5 - - - +
102A TRP* 3.1 25.1 + - + +
162A ALA* 4.3 10.1 - - + +
163A LEU* 4.4 9.6 - - + -
166A HIS* 4.2 24.1 + - + +
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Residues in contact with VAL 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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51A PHE* 5.1 1.3 - - + -
53A LEU* 3.9 26.0 - - + -
95A THR* 3.0 18.5 + - + +
96A LEU* 4.1 3.4 - - - +
98A THR* 1.3 76.5 - - - +
100A GLN* 1.3 59.3 + - + +
102A TRP* 3.1 19.0 + - + +
103A LEU* 2.9 49.7 + - + +
120A LEU* 4.7 4.5 - - + -
163A LEU* 4.2 3.8 - - + -
166A HIS* 4.0 19.1 - - + +
167A VAL* 3.9 23.1 - - + -
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Residues in contact with GLN 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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96A LEU* 2.9 45.2 + - + +
97A HIS* 3.7 18.5 - - - +
99A VAL* 1.3 77.8 - - - +
101A LYS* 1.3 57.7 + - + +
103A LEU* 3.3 4.4 + - - +
104A LEU* 2.9 32.0 + - - +
120A LEU* 4.5 19.8 - - + +
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Residues in contact with LYS 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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97A HIS* 3.0 44.0 + - - +
98A THR* 4.0 6.2 - - - +
100A GLN* 1.3 76.0 - - + +
102A TRP* 1.3 62.7 + - - +
104A LEU* 3.5 6.3 + - - +
105A ALA* 3.0 26.7 + - - +
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Residues in contact with TRP 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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51A PHE* 3.7 34.5 - + - -
98A THR* 3.1 20.3 + - + +
99A VAL* 3.1 8.7 + - + +
101A LYS* 1.3 76.3 - - - +
103A LEU* 1.3 77.5 + - + +
105A ALA* 3.6 6.1 - - - +
106A ALA* 3.3 19.9 + - - +
132A LEU* 3.3 38.5 + - + +
133A LEU* 4.0 0.4 - - + -
159A LEU* 3.5 28.3 - - + -
160A PRO* 4.0 13.6 - - + +
163A LEU* 3.0 42.3 - - + +
167A VAL* 4.4 8.3 - - + -
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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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51A PHE* 3.5 45.3 - - + -
99A VAL* 2.9 34.1 + - + +
100A GLN* 3.9 3.8 - - - +
102A TRP* 1.3 83.4 - - + +
104A LEU* 1.3 66.3 + - - +
106A ALA* 3.1 5.8 + - - +
107A GLY 3.1 6.6 + - - -
108A ALA* 3.0 37.9 + - + +
111A CYS* 5.7 0.4 - - - -
120A LEU* 3.9 21.5 - - + -
122A CYS* 4.0 13.9 - - - -
124A LEU* 5.2 1.8 - - + -
132A LEU* 3.8 15.7 - - + -
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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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100A GLN 2.9 18.0 + - - +
101A LYS* 4.0 5.6 - - - +
103A LEU* 1.3 75.1 - - - +
105A ALA* 1.3 64.5 + - - +
107A GLY* 3.0 16.3 + - - -
108A ALA* 4.5 15.5 - - - +
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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 LYS 3.0 18.2 + - - +
102A TRP* 3.6 7.2 - - - +
104A LEU* 1.3 78.7 - - - +
106A ALA* 1.3 58.7 + - - +
107A GLY* 3.4 1.4 + - - -
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Residues in contact with ALA 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 TRP 3.3 4.1 + - - +
103A LEU* 3.1 10.1 + - - +
105A ALA* 1.3 76.9 - - - +
107A GLY* 1.3 57.1 + - - +
108A ALA 3.7 0.4 - - - -
124A LEU* 4.0 6.2 - - + +
128A GLN* 3.3 32.1 + - - +
131A LEU* 6.4 0.2 - - + -
132A LEU* 3.5 40.4 - - + +
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Residues in contact with GLY 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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104A LEU* 3.0 12.9 + - - -
105A ALA 3.2 1.9 - - - -
106A ALA* 1.3 79.6 - - - +
108A ALA* 1.3 68.3 + - - +
109A GLN* 3.5 13.4 + - - +
123A TRP 4.1 2.1 - - - +
124A LEU* 4.0 3.6 - - - -
128A GLN* 3.6 25.2 + - - +
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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