Contacts of the strand formed by residues 96 - 102 (chain B) in PDB entry 3BEQ
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 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B ILE* 3.7 2.8 - - - +
95B SER* 1.3 80.9 + - - +
97B TRP* 1.3 72.8 + - - -
361B TRP* 4.5 2.2 - - - -
395B GLN* 3.6 11.2 - - - -
448B GLY* 3.4 5.0 - - - -
449B VAL 2.9 27.7 + - - +
453B THR* 3.7 16.2 - - - -
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Residues in contact with TRP 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ILE* 3.4 26.0 - - + -
96B GLY* 1.3 77.9 - - - -
98B ALA* 1.3 59.3 + - - +
99B ILE 4.2 0.3 + - - -
354B PHE* 3.8 23.8 - + - -
361B TRP* 3.3 39.8 - + + -
376B MET* 3.6 35.2 - - + +
395B GLN* 2.9 45.7 + - - +
397B ILE* 4.9 1.1 - - + -
420B PRO* 3.5 17.5 - - + -
421B CYS* 4.2 0.9 - - - -
422B PHE* 3.6 28.9 - + + -
446B PHE* 4.0 18.3 - - + -
447B CYS* 3.5 7.4 - - - -
448B GLY* 3.4 28.9 - - - -
453B THR* 3.6 11.0 - - - +
454B VAL 4.6 1.9 + - - +
458B TRP* 6.0 0.3 - - - -
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLY 4.2 0.4 + - - -
97B TRP* 1.3 73.4 - - - +
99B ILE* 1.3 66.3 + - - +
100B TYR* 4.3 0.2 - - - -
446B PHE* 3.2 3.6 - - - -
447B CYS* 2.9 37.1 + - + +
449B VAL* 4.1 22.9 - - + -
452B ASP 5.8 0.7 - - - +
453B THR* 4.0 6.4 - - + +
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Residues in contact with ILE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B TRP 4.2 0.4 + - - -
98B ALA* 1.3 74.7 - - - +
100B TYR* 1.3 62.0 + - - +
101B SER* 4.0 16.6 - - - +
102B LYS* 4.9 5.6 - - + -
444B ILE* 4.8 3.6 - - + -
445B SER 3.6 8.7 - - - +
446B PHE* 3.5 26.6 - - + -
458B TRP* 3.5 57.6 - - + +
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Residues in contact with TYR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ALA 3.4 1.0 + - - +
99B ILE* 1.3 76.0 - - - +
101B SER* 1.3 63.6 + - - +
122B ILE* 5.1 0.2 - - + -
129B CYS* 3.8 17.1 - - + +
163B VAL* 4.2 18.1 - - + +
410B PHE* 4.2 17.9 - + - -
412B GLN* 3.2 30.9 + - - -
445B SER* 2.7 34.3 + - - +
446B PHE* 4.1 10.8 - - - +
447B CYS* 4.2 13.2 - - + +
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Residues in contact with SER 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ILE* 3.9 7.3 - - - +
100B TYR* 1.3 82.4 - - - +
102B LYS* 1.3 64.4 + - - +
122B ILE* 4.1 3.6 - - - +
163B VAL* 3.3 32.3 - - - +
164B GLY* 4.3 9.7 + - - -
443B SER* 5.2 4.0 + - - -
444B ILE* 3.3 7.0 - - - +
445B SER* 2.6 46.5 + - - +
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ILE* 4.9 5.6 - - + -
101B SER* 1.3 77.6 - - - +
103B ASP* 1.3 63.8 + - - +
104B ASN* 2.8 43.0 + - - +
164B GLY* 3.7 11.3 - - - +
426B LEU* 4.8 2.0 - - - +
442B SER* 4.9 2.4 + - - -
443B SER 3.4 7.2 - - - +
444B ILE* 3.6 17.1 - - + +
458B TRP* 3.9 30.1 - - + +
459B PRO* 3.0 30.7 + - - -
460B ASP* 3.4 11.1 + - - +
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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