Contacts of the helix formed by residues 95 - 108 (chain A) in PDB entry 5DQZ
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 ARG 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A GLY* 3.5 1.0 - - - -
94A ALA* 1.3 86.5 - - + +
96A SER* 1.3 66.4 + - - +
97A ASP* 2.5 36.9 + - - +
98A LYS* 3.5 37.8 - - + +
99A LEU* 3.4 26.6 + - - +
198A ALA 5.9 0.2 - - - -
199A GLY* 4.7 8.2 + - - +
280A PRO* 4.2 4.8 + - - +
281A ALA* 3.8 27.7 - - - +
203B ALA* 4.7 0.4 - - - -
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Residues in contact with SER 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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94A ALA 4.0 1.4 + - - -
95A ARG* 1.3 71.6 - - - +
97A ASP* 1.3 59.4 + - - +
99A LEU* 3.3 6.6 + - - +
100A LEU* 2.9 46.4 + - - +
203B ALA* 3.2 30.7 + - - +
204B ILE* 4.9 4.0 - - - -
210B GLY* 3.7 28.3 - - - -
211B LYS 3.8 8.0 + - - -
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Residues in contact with ASP 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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95A ARG* 2.5 50.4 + - - +
96A SER* 1.3 75.3 + - - +
98A LYS* 1.3 61.1 + - - -
100A LEU* 3.8 8.0 - - - +
101A TYR* 2.9 29.7 + - - +
280A PRO* 3.2 22.1 - - + +
281A ALA* 4.8 1.0 + - - +
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Residues in contact with LYS 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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95A ARG* 3.5 46.9 - - + +
96A SER 3.3 0.4 - - - -
97A ASP* 1.3 82.0 + - - +
99A LEU* 1.3 61.1 + - - +
101A TYR* 3.1 5.8 + - - +
102A GLN 3.0 24.8 + - - -
198A ALA* 2.8 27.7 + - - +
199A GLY 3.3 19.3 - - - +
200A TYR* 3.4 28.4 - - + +
269A GLU* 3.1 22.2 + - - -
280A PRO* 3.8 20.6 - - + -
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Residues in contact with LEU 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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92A GLY 3.3 27.1 - - - +
93A GLY* 4.3 13.0 - - - +
95A ARG 3.4 16.1 + - - +
96A SER 3.3 4.7 + - - +
98A LYS* 1.3 76.7 - - - +
100A LEU* 1.3 57.4 + - - +
102A GLN* 3.5 7.7 + - - +
103A ALA* 2.9 30.6 + - - +
199A GLY 3.7 17.0 - - - +
200A TYR* 4.0 2.0 - - - -
201A ALA* 3.8 31.4 - - + +
204A ILE* 5.4 3.5 - - + +
201B ALA* 4.3 15.9 - - + -
203B ALA* 4.4 9.6 - - + -
204B ILE* 4.1 16.8 - - + +
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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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96A SER* 2.9 32.3 + - - +
97A ASP* 4.0 6.7 - - - +
99A LEU* 1.3 72.8 - - - +
101A TYR* 1.3 60.6 + - - +
103A ALA* 4.2 2.0 - - - -
104A LYS* 2.9 32.6 + - - +
103B ALA* 4.3 11.4 - - + +
106B ALA* 4.8 4.3 - - + -
107B LEU* 3.9 37.4 - - + +
204B ILE* 4.0 34.5 - - + -
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Residues in contact with TYR 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 ASP 2.9 19.9 + - - +
98A LYS* 3.3 5.4 - - - +
100A LEU* 1.3 76.2 - - - +
102A GLN* 1.3 65.1 + - - +
104A LYS* 3.8 5.3 - - + +
105A LEU* 3.0 39.9 + - + +
200A TYR* 3.6 25.6 - + - -
269A GLU* 4.8 5.0 + - - -
272A LEU* 3.2 42.6 + - + -
273A ALA* 3.4 10.2 + - - -
277A ILE* 3.6 35.1 + - + -
278A GLN 3.7 21.1 - - - -
279A PRO* 4.1 11.8 - - + +
280A PRO* 4.2 15.0 - - + -
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Residues in contact with GLN 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 LYS 3.0 15.2 + - - +
99A LEU* 3.7 8.8 - - - +
101A TYR* 1.3 77.1 - - - +
103A ALA* 1.3 58.1 + - - +
105A LEU* 3.2 14.2 + - - +
106A ALA* 2.9 25.8 + - - +
200A TYR* 3.5 18.2 - - + +
201A ALA* 2.8 51.1 + - - +
204A ILE* 3.0 34.3 + - + +
206A PHE* 3.9 11.5 - - + -
215A PHE* 3.4 17.8 - - - -
272A LEU* 4.8 5.8 - - + -
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Residues in contact with ALA 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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99A LEU 2.9 18.9 + - - +
100A LEU* 4.0 4.9 - - - +
102A GLN* 1.3 74.1 - - - +
104A LYS* 1.3 61.1 + - - +
106A ALA* 3.1 2.7 + - - +
107A LEU* 2.9 37.2 + - + +
204A ILE* 4.7 8.5 - - + +
100B LEU* 4.3 16.6 - - + -
103B ALA* 3.5 31.6 - - + -
107B LEU* 5.1 1.1 - - + -
204B ILE* 6.0 0.2 - - + -
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Residues in contact with LYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A LEU 2.9 19.7 + - - +
101A TYR* 3.8 5.8 - - + +
103A ALA* 1.3 75.0 - - - +
105A LEU* 1.3 63.8 + - + +
107A LEU* 4.0 4.3 - - - +
108A ASP* 3.3 26.4 + - + +
111A LEU* 3.9 12.9 - - + +
277A ILE* 4.8 27.4 - - + +
107B LEU* 4.1 24.3 - - + +
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Residues in contact with LEU 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 TYR* 3.0 36.0 + - + +
102A GLN* 3.3 8.1 - - - +
104A LYS* 1.3 79.4 - - + +
106A ALA* 1.3 60.4 + - - +
108A ASP 3.5 2.8 - - - +
111A LEU* 3.8 20.0 - - + +
112A ARG* 3.1 28.8 + - - -
115A VAL* 4.4 5.6 - - + -
206A PHE* 3.7 12.6 - - + -
272A LEU* 3.5 46.2 - - + +
275A GLY* 3.9 27.1 - - - -
277A ILE* 4.6 13.7 - - + -
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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 GLN 2.9 16.4 + - - +
103A ALA 3.1 4.9 + - - +
105A LEU* 1.3 77.2 - - - +
107A LEU* 1.3 62.2 + - - +
108A ASP 3.5 0.6 + - - -
112A ARG* 4.0 19.1 - - - +
204A ILE* 3.8 25.1 - - + -
205A GLY 4.7 5.4 - - - +
206A PHE* 3.6 18.8 - - + -
100B LEU* 3.9 13.6 - - + +
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Residues in contact with LEU 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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103A ALA 2.9 22.6 + - - +
104A LYS* 4.0 4.5 - - - +
106A ALA* 1.3 76.6 - - - +
108A ASP* 1.3 61.1 + - - +
109A GLU* 3.6 11.6 + - - +
100B LEU* 4.1 33.7 - - + +
103B ALA* 4.4 4.5 - - + -
104B LYS* 3.6 52.7 - - + +
107B LEU* 4.6 10.1 - - + -
280B PRO* 4.5 10.8 - - + -
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Residues in contact with ASP 108 (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 LYS* 3.3 8.1 + - + +
105A LEU 3.5 0.3 - - - +
107A LEU* 1.3 78.3 - - + +
109A GLU* 1.3 82.3 + - - +
110A ASP* 3.6 11.7 + - - +
111A LEU* 3.3 42.3 + - + +
112A ARG* 2.8 35.8 + - - +
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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