Contacts of the strand formed by residues 96 - 101 (chain B) in PDB entry 5LS6
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 LEU 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B GLU* 3.2 22.9 - - + +
92B HIS* 3.9 21.3 - - + +
95B PRO* 1.3 69.7 - - - +
97B PHE* 1.3 61.8 + - - +
98B GLY 3.5 2.2 - - - +
115B THR* 4.3 4.7 - - - +
116B VAL 3.2 15.7 - - - +
117B GLY* 4.1 3.6 - - - -
414B ARG* 3.3 22.4 - - - +
428B VAL* 3.4 32.8 - - + +
429B CYS 2.9 13.4 + - - +
432B ALA* 3.8 17.5 - - - +
433B SER 3.7 7.4 - - - +
434B ILE* 3.4 36.3 - - + -
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Residues in contact with PHE 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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95B PRO* 3.4 34.0 + - + -
96B LEU* 1.3 72.7 - - - +
98B GLY* 1.3 56.7 + - - +
116B VAL 3.0 5.3 + - - -
146B ASN* 3.8 21.3 - - - -
147B PHE 3.7 10.1 - - - +
148B TYR* 3.2 44.0 - + - +
365B TYR* 4.1 21.1 - + + -
367B ARG* 4.4 4.3 + - - -
414B ARG* 3.5 47.4 - - + +
415B GLN* 4.1 8.3 - - - +
428B VAL* 4.9 0.2 - - - -
7Q M3L 3.6 29.2 - - - -
8Q PHE* 3.8 20.9 - + - -
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Residues in contact with GLY 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU 3.5 0.4 - - - -
97B PHE* 1.3 80.4 - - - +
99B VAL* 1.3 60.2 + - - +
100B GLN* 6.1 0.2 - - - -
115B THR* 3.4 4.3 - - - -
116B VAL* 2.9 45.5 + - - +
148B TYR 3.5 6.1 + - - -
149B THR* 4.7 4.9 - - - -
150B CYS* 4.7 3.1 - - - -
367B ARG* 5.8 0.9 - - - -
415B GLN* 3.3 8.1 - - - -
428B VAL* 4.2 4.5 - - - +
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Residues in contact with VAL 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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98B GLY* 1.3 73.3 - - - +
100B GLN* 1.3 79.3 + - - +
113B PHE* 4.0 6.5 - - + -
114B ALA 3.4 11.9 - - - +
115B THR* 4.0 6.3 - - + -
150B CYS* 4.7 1.4 - - - -
415B GLN* 2.7 49.9 + - - +
416B THR* 4.0 1.3 - - - -
417B SER* 3.4 20.2 - - - +
426B ILE* 3.6 28.7 - - + -
428B VAL* 3.7 22.4 - - + +
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Residues in contact with GLN 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 GLY* 6.1 0.2 - - - -
99B VAL* 1.3 89.4 + - - +
101B PHE* 1.3 59.2 + - - +
113B PHE* 3.9 4.5 - - - -
114B ALA 3.0 25.3 + - - -
150B CYS* 3.2 43.1 - - - +
151B ALA* 4.2 10.9 - - - +
152B TRP* 2.6 37.7 + - + -
196B LEU 5.4 1.4 - - - +
197B LYS* 5.5 6.9 - - - +
369B SER* 6.1 2.0 - - - -
415B GLN* 3.9 17.1 - - - +
416B THR 5.1 1.0 + - - -
417B SER* 3.7 9.5 + - - +
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Residues in contact with PHE 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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100B GLN* 1.3 74.5 + - - +
102B ASN* 1.3 60.4 + - - +
103B TRP* 3.3 23.3 + - + +
111B LEU* 4.2 15.3 - - + -
112B VAL 3.0 26.5 - - - -
113B PHE* 3.7 14.8 - + + -
126B CYS* 4.3 4.0 - - - -
152B TRP* 3.2 10.9 - - - +
417B SER* 2.8 38.3 + - - +
418B PHE 2.9 27.6 - - - +
419B SER* 3.5 25.6 - - - -
420B ARG 5.0 0.2 - - - -
424B ILE* 3.7 17.3 - - + -
426B ILE* 3.3 32.8 - - + -
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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