Contacts of the helix formed by residues 89 - 101 (chain A) in PDB entry 5W0P
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 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A PHE* 3.0 12.7 + - - +
88A LEU* 1.3 82.5 - - - +
90A GLY* 1.3 60.6 + - - +
93A SER* 2.9 27.9 + - - -
113A GLN* 4.1 6.1 - - - +
116A PHE* 4.0 27.3 - - - -
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Residues in contact with GLY 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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85A PHE 3.3 5.8 + - - -
86A MET* 3.2 12.6 + - - -
89A GLY* 1.3 77.2 - - - +
91A PHE* 1.3 60.9 + - - +
94A THR* 2.6 38.3 + - - -
113A GLN* 3.9 20.0 - - - +
116A PHE* 4.5 1.8 - - - +
117A ALA* 4.7 9.0 - - - -
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Residues in contact with PHE 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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44A MET* 3.4 27.6 - - + +
47A LEU* 3.8 23.1 - - + -
48A ILE* 3.6 15.7 - - + +
86A MET* 2.7 36.9 + - + -
87A VAL* 3.4 31.3 + - + +
90A GLY* 1.3 74.7 - - - +
92A THR* 1.3 59.9 + - - +
94A THR* 3.7 1.5 - - - -
95A LEU* 2.8 31.0 + - - +
117A ALA* 6.0 3.6 - - + -
296A LYS* 3.6 50.9 - - + -
299A ALA* 3.8 18.6 - - + -
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Residues in contact with THR 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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48A ILE* 3.7 19.4 - - + +
87A VAL* 2.8 22.3 + - - +
88A LEU* 3.0 23.4 + - + +
90A GLY 3.4 0.4 - - - -
91A PHE* 1.3 79.1 - - - +
93A SER* 1.3 60.5 + - - +
95A LEU* 3.6 6.2 - - + +
96A TYR* 3.4 20.1 + - - +
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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 LEU 4.8 1.6 + - - -
89A GLY* 2.9 20.1 + - - -
90A GLY 3.5 1.0 + - - -
91A PHE 3.4 0.2 - - - -
92A THR* 1.3 74.3 - - - +
94A THR* 1.3 64.4 + - - +
95A LEU 3.2 0.2 - - - -
96A TYR* 3.2 5.1 + - - +
97A THR* 3.1 27.2 + - - +
105A PHE* 3.9 20.1 - - - -
113A GLN* 3.3 23.4 - - - +
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Residues in contact with THR 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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40A LEU* 4.9 6.1 - - + -
44A MET* 3.9 31.2 - - + +
90A GLY 2.6 24.9 + - - -
91A PHE* 3.8 4.3 - - - -
92A THR 3.4 0.2 - - - -
93A SER* 1.3 75.8 - - - +
95A LEU* 1.3 51.8 + - - +
97A THR* 2.9 19.1 + - - -
98A SER* 2.7 24.2 + - - -
113A GLN* 2.9 18.7 + - - +
185A CYS 4.1 5.4 - - - +
186A SER* 3.6 29.9 + - - +
296A LYS* 4.3 1.8 + - - +
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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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41A ALA* 3.1 30.3 - - - +
44A MET* 4.3 5.4 - - + -
45A PHE* 4.0 26.0 - - + +
48A ILE* 3.7 22.7 - - + -
91A PHE 2.8 18.8 + - - +
92A THR* 3.6 8.7 - - + +
94A THR* 1.3 78.2 - - - +
96A TYR* 1.3 57.8 + - - +
98A SER* 2.7 18.1 + - - -
99A LEU* 3.0 40.7 + - + +
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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 THR 3.4 9.2 + - - +
93A SER* 3.2 9.7 + - - +
95A LEU* 1.3 81.7 - - - +
97A THR* 1.3 60.0 + - - +
99A LEU* 3.3 30.2 - - + +
100A HIS* 3.4 38.4 + + - -
104A VAL* 4.5 17.3 - - + -
105A PHE* 3.4 33.4 - + + -
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Residues in contact with THR 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 11.7 + - - +
94A THR 2.9 20.4 + - - -
96A TYR* 1.3 73.2 - - - +
98A SER* 1.3 54.1 + - - +
99A LEU 3.1 1.6 - - - -
100A HIS 3.3 1.8 + - - +
101A GLY 2.8 31.2 + - - -
102A TYR 3.2 27.8 + - - +
103A PHE* 3.8 26.9 - - + -
104A VAL* 3.9 4.3 - - + +
105A PHE* 3.8 22.7 - - + -
185A CYS* 2.6 28.7 + - - +
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Residues in contact with SER 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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37A PHE* 3.4 36.6 - - - +
38A SER* 4.5 0.9 + - - -
40A LEU* 4.1 20.7 + - - -
41A ALA* 3.5 19.3 - - - +
44A MET* 4.6 0.5 - - - +
94A THR 2.7 14.6 + - - -
95A LEU* 2.7 24.3 + - - -
97A THR* 1.3 77.9 + - - +
99A LEU* 1.3 65.3 + - - +
101A GLY 3.8 3.7 + - - -
185A CYS* 4.0 12.3 - - - +
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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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29A TYR* 4.0 5.9 + - - -
37A PHE* 5.8 0.2 - - - +
41A ALA* 3.9 18.8 - - + -
95A LEU* 3.0 32.7 + - + +
96A TYR* 3.3 32.3 - - + +
97A THR 3.1 0.2 - - - -
98A SER* 1.3 80.0 - - - +
100A HIS* 1.3 70.7 + - + +
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Residues in contact with HIS 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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27A PRO* 5.0 0.7 - - - +
29A TYR* 2.7 25.8 + - - -
96A TYR* 3.4 57.7 + + - -
97A THR 3.3 4.9 + - - +
99A LEU* 1.3 83.5 - - + +
101A GLY* 1.3 55.2 + - - +
102A TYR* 3.4 18.9 + + + -
104A VAL* 4.1 20.6 - - + -
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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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27A PRO* 4.9 0.2 - - - -
28A GLN* 3.8 14.0 + - - +
29A TYR* 3.5 17.8 + - - -
37A PHE* 3.2 35.0 - - - -
97A THR 2.8 8.0 + - - -
98A SER 3.8 2.7 + - - -
99A LEU 3.3 2.4 - - - -
100A HIS* 1.3 78.5 - - - +
102A TYR* 1.3 60.4 + - - +
185A CYS* 3.2 9.5 - - - -
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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