Contacts of the strand formed by residues 96 - 101 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90H GLU* 3.1 26.9 - - + +
92H HIS* 3.9 20.2 - - + +
95H PRO* 1.3 72.3 - - - +
97H PHE* 1.3 55.7 + - - +
98H GLY 3.3 5.6 - - - +
115H THR* 3.7 13.5 - - - +
116H VAL 3.3 24.0 - - - +
117H GLY* 3.9 3.1 - - - +
120H ARG 5.3 0.2 - - - +
414H ARG* 3.5 11.7 - - - +
428H VAL* 3.3 37.0 - - + +
429H CYS 3.0 11.8 + - - +
432H ALA* 4.0 18.2 - - - +
433H SER 4.1 4.9 - - - +
434H ILE* 3.9 27.4 - - + -
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Residues in contact with PHE 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H PRO* 3.7 29.2 - - + -
96H LEU* 1.3 71.0 - - - +
98H GLY* 1.3 56.1 + - - +
116H VAL 3.0 6.1 + - - -
118H SER 5.7 0.4 - - - -
146H ASN* 4.1 20.9 - - - -
147H PHE 3.9 7.0 - - - +
148H TYR* 3.4 37.8 - + - +
365H TYR* 3.6 22.1 - + + -
367H ARG* 4.0 3.6 + - - -
414H ARG* 3.7 45.3 - - + +
415H GLN* 3.9 7.6 - - - +
7S M3L 3.4 42.6 - - - -
8S PHE* 3.6 20.0 - + - -
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Residues in contact with GLY 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96H LEU 3.3 2.1 + - - -
97H PHE* 1.3 82.4 - - - +
99H VAL* 1.3 65.1 + - - +
115H THR* 3.7 4.7 - - - -
116H VAL* 3.4 41.0 + - - +
148H TYR 4.0 2.5 - - - -
149H THR* 5.2 2.2 - - - -
150H CYS* 4.9 1.3 - - - -
415H GLN* 3.1 12.8 - - - -
428H VAL* 3.8 8.5 - - - +
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Residues in contact with VAL 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98H GLY* 1.3 75.1 - - - +
100H GLN* 1.3 86.7 + - - +
113H PHE* 4.1 9.6 - - + -
114H ALA 3.3 15.9 - - - +
115H THR* 4.4 0.4 - - + -
150H CYS* 4.7 1.5 - - - -
415H GLN* 3.1 40.9 + - + +
416H THR* 3.8 14.6 - - - -
417H SER* 3.8 7.0 - - - +
426H ILE* 3.9 22.2 - - + +
428H VAL* 3.5 26.7 - - + -
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Residues in contact with GLN 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H VAL* 1.3 97.3 + - - +
101H PHE* 1.3 59.7 + - - +
113H PHE* 3.9 2.9 - - - -
114H ALA 2.7 35.8 + - - -
150H CYS* 3.3 39.6 - - - +
151H ALA* 4.3 9.8 - - - +
152H TRP* 2.9 24.8 + - + +
196H LEU 5.6 0.5 - - - +
197H LYS* 5.4 7.4 - - - -
415H GLN* 4.4 14.1 + - - +
416H THR 5.0 1.6 + - - -
417H SER* 3.7 10.1 + - - -
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Residues in contact with PHE 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H GLN* 1.3 73.6 - - - +
102H ASN* 1.3 63.4 + - - +
103H TRP* 3.4 31.4 + - + +
111H LEU* 3.7 25.6 - - + -
112H VAL 3.5 11.0 - - - -
113H PHE* 3.7 24.2 - + + -
126H CYS* 3.9 10.8 - - - -
152H TRP* 3.2 10.8 - - - -
417H SER* 3.2 35.9 + - - -
418H PHE 3.4 17.5 - - - +
419H SER* 3.7 17.9 - - - -
424H ILE* 4.2 13.7 - - + -
426H ILE* 3.3 32.5 - - + -
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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