Contacts of the strand formed by residues 85 - 90 (chain A) in PDB entry 3L75
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 HIS 85 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLY 4.0 0.9 + - - -
84A ALA* 1.3 75.6 - - - +
86A PHE* 1.3 61.7 + - - +
87A ASN* 4.0 2.5 - - + -
98A TYR* 3.7 1.4 - - - +
99A ILE* 3.2 10.4 - - - +
100A LYS* 2.9 55.7 + - + +
283B PRO 5.1 3.7 + - - -
284B LEU* 3.2 42.3 - - + +
367B THR* 4.8 8.3 + - - -
370B MET* 3.3 34.4 - - + +
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Residues in contact with PHE 86 (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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64A PHE* 3.1 40.1 - + - -
75A PHE* 3.3 34.8 - + - -
79A VAL* 4.4 12.1 - - + -
84A ALA 4.1 0.8 + - - -
85A HIS* 1.3 73.0 - - - +
87A ASN* 1.3 60.7 + - - +
97A PHE* 4.3 3.1 - - + -
98A TYR 3.1 25.8 - - - -
99A ILE* 3.3 32.8 - - + -
112A LEU* 5.5 0.9 - - + -
113A LEU* 4.1 11.9 - - + -
116A VAL* 3.9 17.0 - - + -
284B LEU 2.7 13.6 + - - +
285B ILE* 3.6 16.2 - - + -
286B LYS* 3.0 27.4 + - - +
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Residues in contact with ASN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 3.5 14.8 - - - -
85A HIS* 4.0 3.2 + - + -
86A PHE* 1.3 75.4 - - - +
88A GLY* 1.3 76.1 + - - +
89A TYR* 5.5 2.0 - - - +
98A TYR* 2.9 69.1 + - + +
286B LYS* 3.1 26.6 - - - +
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Residues in contact with GLY 88 (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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60A GLU* 4.4 4.5 - - - -
64A PHE* 4.1 6.7 - - - -
87A ASN* 1.3 87.5 + - - +
89A TYR* 1.3 59.7 + - - +
96A ALA 3.0 15.9 - - - -
97A PHE* 4.2 3.4 - - - -
98A TYR* 4.4 5.4 - - - -
286B LYS* 2.5 36.9 + - - +
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Residues in contact with TYR 89 (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 TRP* 3.4 2.9 + - - -
60A GLU* 3.2 13.9 + - - +
87A ASN* 5.5 2.2 - - - +
88A GLY* 1.3 77.7 - - - +
90A THR* 1.3 70.3 + - - +
91A SER* 4.3 7.6 - - - -
94A GLN* 2.8 34.6 + - + -
95A THR* 3.2 6.2 - - - +
96A ALA* 2.9 53.3 + - + -
98A TYR* 4.5 12.3 - + - -
377A GLU* 2.8 40.9 + - - -
286B LYS* 4.4 3.8 - - - +
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Residues in contact with THR 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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44A GLY* 4.6 4.5 - - - -
45A SER 5.1 0.5 + - - -
56A GLY* 4.1 15.7 + - - -
57A TYR* 3.6 26.8 - - + -
60A GLU* 2.9 32.4 + - + +
89A TYR* 1.3 79.1 - - - +
91A SER* 1.3 68.4 + - - +
94A GLN 3.8 4.3 - - - -
95A THR* 3.9 18.4 + - - -
167A VAL* 3.1 22.1 - - + +
185A TYR* 5.4 0.2 + - - -
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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