Contacts of the strand formed by residues 98 - 104 (chain A) in PDB entry 1QL6
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 PHE 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A THR* 5.4 3.1 - - - -
49A ILE* 3.8 21.3 - - + -
50A ILE 3.2 11.2 - - - -
51A ASP* 3.4 35.4 - - + -
52A VAL* 5.0 0.2 - - - -
94A GLU* 3.6 1.6 - - - -
95A THR* 2.9 38.1 + - - +
97A THR* 1.3 95.2 + - - +
99A PHE* 1.3 64.1 + - - +
100A PHE* 3.4 29.4 - + + -
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Residues in contact with PHE 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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48A LYS 4.1 0.7 - - - -
49A ILE* 3.4 5.7 - - - +
50A ILE* 2.8 38.2 + - + +
52A VAL* 3.3 35.0 - - + -
67A ARG* 3.6 36.3 - - + -
70A THR* 3.8 32.3 - - + -
71A LEU* 4.1 14.8 - - + -
74A VAL* 5.5 4.0 - - + -
92A THR* 5.9 2.5 - - - -
93A TYR 3.6 5.8 - - - -
94A GLU* 3.4 43.3 - - + -
95A THR 5.8 1.1 - - - -
98A PHE* 1.3 75.2 - - - +
100A PHE* 1.3 65.4 + - - +
101A LEU* 4.4 11.4 - - + -
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Residues in contact with PHE 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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12A THR* 4.2 16.6 - - + -
15A PHE* 3.4 55.9 - + + -
16A TYR* 3.8 29.6 - + - -
47A VAL* 4.2 3.1 - - + -
48A LYS 3.5 3.8 - - - -
49A ILE* 4.1 22.0 - - + -
91A ASP 3.6 0.3 - - - +
92A THR* 3.3 24.1 - - - -
93A TYR* 3.0 28.5 + - + +
95A THR* 4.3 4.7 - - + -
98A PHE* 3.4 35.0 - + + -
99A PHE* 1.3 78.1 - - - +
101A LEU* 1.3 64.2 + - - +
102A VAL* 3.7 1.8 + - - +
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Residues in contact with LEU 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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47A VAL* 3.1 2.9 - - - -
48A LYS* 2.6 47.5 + - + +
50A ILE* 4.4 13.5 - - + -
70A THR* 4.5 5.2 - - + -
73A GLU* 4.2 26.0 - - + +
74A VAL* 3.6 34.3 - - + -
77A LEU* 4.2 13.0 - - + -
89A LEU* 3.5 13.9 - - + -
91A ASP 3.6 2.0 - - - -
92A THR* 3.7 9.4 - - + -
99A PHE* 4.4 13.0 - - + -
100A PHE* 1.3 84.6 - - - +
102A VAL* 1.3 63.0 + - - +
103A PHE* 3.5 16.3 - - + -
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Residues in contact with VAL 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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15A PHE* 3.3 37.5 - - + -
19A TYR* 3.7 24.0 - - + +
36A CYS* 5.0 1.3 - - - -
45A TYR* 3.8 28.3 - - + -
46A ALA 3.5 3.4 - - - +
47A VAL* 4.2 2.7 - - + +
89A LEU* 3.5 5.5 - - - +
90A LYS* 2.7 34.0 + - + -
91A ASP* 2.8 36.8 + - + +
93A TYR* 4.5 1.3 - - + -
100A PHE 4.5 1.8 - - - +
101A LEU* 1.3 75.0 - - - +
103A PHE* 1.3 58.2 + - - +
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Residues in contact with PHE 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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33A VAL* 6.2 0.2 - - + -
45A TYR* 3.1 14.0 - - - +
46A ALA 2.5 38.2 + - - +
47A VAL 5.2 0.2 - - - -
48A LYS* 4.1 21.3 - - + -
73A GLU* 4.7 6.1 - - - -
77A LEU* 3.7 33.7 - - + -
87A ILE* 3.8 30.7 - - + -
88A GLN 3.5 17.0 - - - +
89A LEU* 3.9 9.2 - - + -
90A LYS* 4.0 2.2 - - - -
101A LEU* 3.5 41.7 - - + -
102A VAL* 1.3 74.3 - - - +
104A ASP* 1.3 69.2 + - - +
166A THR* 5.2 5.2 - - - -
167A ASP 6.2 0.7 - - - -
301A ATP 4.0 20.2 - - - +
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Residues in contact with ASP 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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45A TYR* 3.8 12.6 - - - -
46A ALA* 4.0 0.4 - - - +
87A ILE* 4.0 9.8 - - + +
88A GLN* 3.6 29.5 + - - +
90A LYS* 3.6 27.1 + - - +
103A PHE* 1.3 74.9 - - - +
105A LEU* 1.3 61.0 + - - +
106A MET* 3.6 18.3 + - + +
164A LYS* 5.4 4.9 + - - -
301A ATP 2.9 25.1 + - - -
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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