Contacts of the helix formed by residues 89 - 101 (chain A) in PDB entry 5O67
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 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A PRO* 1.3 78.7 - - - +
90A GLN* 1.3 65.2 + - - +
91A SER* 3.9 10.3 - - - +
92A VAL* 3.6 25.1 + - + +
93A SER* 3.2 19.9 + - - -
329A GLU* 3.3 22.0 - - - +
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Residues in contact with GLN 90 (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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88A PRO 4.6 0.2 - - - -
89A ALA* 1.3 70.5 - - - +
91A SER* 1.3 67.1 + - - +
92A VAL 3.1 1.5 + - - -
93A SER* 3.3 8.2 + - - -
94A ASN* 3.1 35.5 + - - +
329A GLU* 3.7 22.3 + - - +
330A ARG* 4.3 10.7 - - - -
374A ALA* 3.6 25.9 - - + +
376A SER 3.3 24.3 + - - +
377A GLU* 3.4 24.4 + - - +
379A LEU 4.9 2.2 + - - -
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Residues in contact with SER 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ALA* 3.9 9.9 - - - +
90A GLN* 1.3 74.4 - - - +
92A VAL* 1.3 58.3 + - - +
94A ASN* 3.6 6.9 + - - +
95A LEU* 3.1 28.2 + - - +
326A ALA* 3.7 15.5 - - - +
328A ASN 2.8 28.6 + - - -
329A GLU 2.9 13.8 + - - -
330A ARG* 4.4 6.7 - - - +
331A MET 3.6 21.3 - - - -
332A SER* 4.1 6.6 - - - -
372A THR* 5.1 0.9 - - - -
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Residues in contact with VAL 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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88A PRO* 5.1 7.4 - - + -
89A ALA* 3.6 31.4 + - + +
90A GLN 3.1 0.6 - - - -
91A SER* 1.3 79.6 - - - +
93A SER* 1.3 66.1 + - - +
95A LEU* 3.2 6.7 + - - +
96A TYR* 3.2 41.6 + - + -
276A THR* 6.0 0.2 - - - +
326A ALA* 4.4 14.4 - - + -
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Residues in contact with SER 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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88A PRO* 4.4 14.6 + - - +
89A ALA 3.2 11.7 + - - -
90A GLN* 3.3 13.2 + - - -
92A VAL* 1.3 79.5 - - - +
94A ASN* 1.3 60.6 + - - +
96A TYR* 3.6 5.8 + - - +
97A ASN* 3.1 38.2 + - - +
105A ASN* 4.7 16.9 - - - +
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Residues in contact with ASN 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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90A GLN* 3.1 29.8 + - - +
91A SER* 4.0 1.4 - - - +
93A SER* 1.3 79.2 - - - +
95A LEU* 1.4 64.3 + - - +
97A ASN* 3.3 13.3 + - - +
98A GLU* 3.0 26.5 + - - +
330A ARG 4.8 0.4 + - - -
372A THR* 3.4 28.2 + - + +
374A ALA* 4.2 16.4 - - - +
380A THR* 3.7 34.2 + - + +
405A TYR* 5.3 4.2 - - - -
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Residues in contact with LEU 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 SER 3.1 17.7 + - - +
92A VAL* 3.2 7.6 + - - +
94A ASN* 1.4 73.7 - - - +
96A TYR* 1.3 62.6 + - + +
98A GLU* 3.4 3.7 + - - +
99A ALA* 3.0 32.7 + - - +
281A VAL* 5.4 10.5 - - + -
324A ALA* 4.8 17.0 - - + -
325A PHE 5.6 2.7 - - - +
326A ALA* 5.9 1.6 - - + +
332A SER* 4.2 18.8 - - - +
372A THR* 4.5 1.5 - - - +
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Residues in contact with TYR 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 VAL* 3.2 35.4 + - + +
93A SER* 3.8 9.6 - - - +
95A LEU* 1.3 81.0 - - + +
97A ASN* 1.3 54.4 + - - +
99A ALA* 4.5 3.6 - - - -
100A SER* 2.6 46.6 + - - +
102A PHE 5.8 0.2 - - - +
217A GLU* 2.6 27.5 + - - -
223A ASP* 4.0 21.3 - - + -
274A VAL* 3.3 31.9 - - + +
276A THR* 2.6 31.7 + - - -
281A VAL* 4.3 11.4 - - + -
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Residues in contact with ASN 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 SER* 3.1 26.5 + - - +
94A ASN* 3.3 14.5 + - - +
96A TYR* 1.3 78.4 - - - +
98A GLU* 1.3 63.1 + - - +
101A GLY* 3.1 23.7 + - - -
102A PHE 3.1 25.1 + - - +
103A ALA* 3.9 14.0 - - + -
104A GLY* 3.5 10.7 - - - +
105A ASN* 5.0 5.8 + - - +
405A TYR* 3.6 21.5 + - - +
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Residues in contact with GLU 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 ASN 3.0 16.0 + - - +
95A LEU* 3.9 4.9 - - - +
97A ASN* 1.3 77.8 - - - +
99A ALA* 1.3 63.5 + - - +
101A GLY* 4.1 2.8 + - - -
334A SER* 6.1 4.5 - - - +
372A THR* 4.6 8.7 - - - +
382A VAL* 3.7 26.3 - - + +
384A ASN* 4.7 13.3 - - - +
401A LYS* 3.1 31.5 + - - -
501A LDA 4.2 10.4 - - - -
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Residues in contact with ALA 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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95A LEU 3.0 19.1 + - - +
96A TYR* 3.9 3.1 - - - +
98A GLU* 1.3 79.7 - - - +
100A SER* 1.3 57.9 + - - +
272A SER* 4.5 1.4 + - - -
274A VAL* 4.4 11.0 - - + +
281A VAL* 6.0 1.6 - - + -
283A PHE* 3.9 48.5 - - + +
284A GLY 5.7 0.7 - - - +
501A LDA 3.3 22.0 - - - -
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Residues in contact with SER 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 TYR* 2.6 33.1 + - - +
99A ALA* 1.3 73.2 - - - +
101A GLY* 1.3 61.6 + - - +
102A PHE* 3.3 26.6 + - - +
213A LYS* 6.1 0.6 - - - -
223A ASP* 5.7 4.5 - - - -
225A VAL* 4.8 11.5 - - - +
272A SER* 3.4 32.7 + - - -
274A VAL* 4.0 12.6 - - - -
501A LDA 4.1 11.9 - - - +
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Residues in contact with GLY 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 ASN 3.1 14.9 + - - -
98A GLU 4.8 0.2 - - - -
99A ALA 3.5 2.2 + - - -
100A SER* 1.3 76.8 - - - +
102A PHE* 1.3 58.1 + - - +
103A ALA 4.1 1.0 + - - -
157A ARG* 4.9 8.8 + - - -
165A GLN* 3.3 18.4 + - - -
225A VAL* 6.2 0.2 - - - -
501A LDA 4.0 19.5 - - - -
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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