Contacts of the strand formed by residues 96 - 101 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90K GLU* 3.0 26.9 - - - +
92K HIS* 3.8 16.6 - - + +
95K PRO* 1.3 72.2 - - - +
97K PHE* 1.3 58.4 + - - +
98K GLY 4.9 1.6 - - - +
115K THR* 3.8 10.1 - - - +
116K VAL 3.3 14.8 - - - +
117K GLY* 4.1 5.4 - - - +
414K ARG* 3.3 21.3 - - - +
428K VAL* 3.6 30.8 - - + +
429K CYS 3.2 11.7 + - - +
432K ALA* 3.8 22.2 - - - +
433K SER 4.3 0.9 - - - +
434K ILE* 3.6 35.7 - - + -
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Residues in contact with PHE 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K PRO* 3.8 33.2 - - + -
96K LEU* 1.3 72.5 - - - +
98K GLY* 1.3 56.9 + - - +
116K VAL 3.0 5.5 + - - -
146K ASN* 3.9 22.2 - - - -
147K PHE 3.9 9.4 - - - +
148K TYR* 3.3 37.6 - + - +
365K TYR* 3.9 26.6 - + + -
367K ARG* 4.3 4.5 + - - -
414K ARG* 3.4 54.8 - - + +
415K GLN* 4.0 8.7 - - - +
428K VAL* 4.8 0.2 - - - -
7T M3L 3.3 28.0 - - - -
8T PHE* 3.9 13.2 - + - -
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Residues in contact with GLY 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96K LEU 3.6 0.8 - - - -
97K PHE* 1.3 82.2 - - - +
99K VAL* 1.3 63.1 + - - +
115K THR* 3.6 3.8 - - - -
116K VAL* 3.2 42.1 + - - +
148K TYR 3.9 5.1 + - - -
149K THR* 4.9 4.3 - - - -
150K CYS* 4.4 2.7 - - - -
367K ARG* 5.8 0.4 - - - -
415K GLN* 3.1 10.8 - - - -
428K VAL* 4.2 5.5 - - - +
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Residues in contact with VAL 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98K GLY* 1.3 74.0 - - - +
100K GLN* 1.3 87.9 + - - +
113K PHE* 3.8 21.8 - - + -
114K ALA 3.4 15.5 - - - +
115K THR* 4.1 0.7 - - + -
150K CYS* 4.4 2.1 - - - -
415K GLN* 2.7 27.6 + - - +
416K THR* 3.7 28.0 - - - +
417K SER* 3.8 7.6 - - - +
426K ILE* 4.1 11.4 - - + +
428K VAL* 3.8 26.0 - - + -
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Residues in contact with GLN 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K VAL* 1.3 93.6 + - - +
101K PHE* 1.3 65.0 + - - +
103K TRP* 5.6 5.0 - - - -
113K PHE* 4.0 3.1 - - - -
114K ALA 3.0 19.2 + - - -
150K CYS* 3.3 33.4 - - - +
151K ALA* 4.5 5.6 - - + -
152K TRP* 2.7 37.6 + - + +
197K LYS* 6.2 4.3 - - - +
369K SER* 5.1 5.3 - - - -
415K GLN* 3.5 20.4 - - - +
416K THR 4.3 4.4 + - - -
417K SER* 3.5 14.3 + - - +
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Residues in contact with PHE 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100K GLN* 1.3 79.4 - - - +
102K ASN* 1.3 64.6 + - - +
103K TRP* 3.2 19.5 + - + +
111K LEU* 3.8 23.8 - - + -
112K VAL 3.2 24.7 - - - -
113K PHE* 3.7 25.8 - + + -
126K CYS* 3.9 11.4 - - - -
152K TRP* 3.5 7.6 - - - +
417K SER* 3.0 34.4 + - - -
418K PHE 3.4 22.4 - - - +
419K SER* 3.8 21.3 - - - -
424K ILE* 4.3 8.5 - - + -
426K ILE* 3.4 31.0 - - + -
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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