Contacts of the strand formed by residues 105 - 111 (chain A) in PDB entry 5LOH
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 ASN 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A VAL* 5.8 3.1 - - + -
64A VAL 3.7 11.9 - - - +
65A LYS* 5.0 2.0 - - - -
66A LYS* 3.8 6.7 - - - +
101A GLN* 3.7 2.6 - - - +
102A SER* 2.9 28.6 + - - +
103A ALA 3.5 2.2 + - - +
104A ASN* 1.3 80.9 - - - +
106A VAL* 1.3 60.0 + - - +
107A TYR* 3.8 29.3 - - + +
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Residues in contact with VAL 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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63A VAL* 3.6 3.3 - - - -
64A VAL* 2.9 53.4 + - + +
66A LYS* 4.7 4.9 - - + +
99A SER* 5.8 3.1 - - - +
100A LEU 3.8 5.4 - - - +
101A GLN* 4.2 11.0 - - + +
105A ASN* 1.3 73.4 - - - +
107A TYR* 1.3 63.1 + - - +
108A LEU* 6.1 1.1 - - + -
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Residues in contact with TYR 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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32A ILE* 4.7 17.0 - - + -
61A VAL* 4.1 16.4 - - + -
62A LYS 3.6 2.5 - - - -
63A VAL* 3.5 30.7 - - + -
98A TYR 4.0 0.2 - - - +
99A SER* 3.3 7.3 + - - -
100A LEU* 2.6 51.2 + - + +
102A SER* 3.5 32.4 - - - -
105A ASN* 3.8 27.1 - - + +
106A VAL* 1.3 75.7 - - - +
108A LEU* 1.3 64.0 + - - +
109A VAL* 4.1 3.9 + - + +
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Residues in contact with LEU 108 (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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60A ALA 3.3 2.6 - - - +
61A VAL* 3.0 6.7 - - - -
62A LYS* 2.9 56.5 + - + +
64A VAL* 4.5 23.1 - - + -
96A LEU* 3.7 27.4 - - + -
98A TYR 3.7 1.3 - - - -
99A SER* 4.2 20.9 - - - +
106A VAL* 5.5 1.1 - - + -
107A TYR* 1.3 75.1 - - - +
109A VAL* 1.3 62.4 + - - +
110A MET* 3.8 8.2 + - + +
177A LEU* 3.4 30.5 - - + +
178A SER* 5.2 2.0 - - - +
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Residues in contact with VAL 109 (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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35A PHE* 4.2 28.9 - - + -
59A TYR* 3.8 32.1 - - + -
60A ALA 3.8 1.8 - - - -
61A VAL* 4.2 17.5 - - + -
96A LEU* 3.6 1.6 - - - +
97A TYR* 2.6 44.5 + - + +
98A TYR* 3.0 35.1 + - + +
100A LEU* 5.5 4.7 - - + +
107A TYR* 5.0 5.8 - - + +
108A LEU* 1.3 74.4 - - - +
110A MET* 1.3 56.1 - - - +
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Residues in contact with MET 110 (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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49A VAL* 4.9 0.4 - - + -
59A TYR* 3.7 7.6 - - - +
60A ALA* 2.9 51.3 + - + +
61A VAL 4.7 0.2 - - - -
62A LYS* 3.8 22.9 - - + +
94A VAL* 3.7 16.4 - - + -
95A HIS 3.4 12.3 - - - +
96A LEU* 4.1 21.5 - - + +
97A TYR* 4.1 5.6 - - - +
108A LEU* 4.0 11.0 - - + +
109A VAL* 1.3 77.7 - - - +
111A GLU* 1.3 63.8 + - - +
112A TYR 3.5 0.2 + - - -
173A THR* 4.5 0.2 - - - -
177A LEU* 4.4 15.3 - - + -
901A STU 3.6 48.0 - - + -
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Residues in contact with GLU 111 (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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58A LEU 5.2 0.2 - - - -
59A TYR* 4.9 1.1 - - - -
60A ALA 4.3 0.2 - - - -
94A VAL* 4.1 5.2 - - + +
95A HIS* 2.9 43.1 + - - +
97A TYR* 3.9 27.7 + - + +
110A MET* 1.3 73.7 - - - +
112A TYR* 1.3 60.4 + - - +
113A LEU* 3.4 23.5 + - + +
171A LYS* 2.6 36.0 + - - +
901A STU 3.0 22.7 + - - -
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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