Contacts of the strand formed by residues 255 - 260 (chain B) in PDB entry 6HBU
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 SER 255 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B ILE 4.6 4.1 + - - -
71B MET* 5.3 0.8 - - - +
72B LYS 6.0 0.9 - - - -
75B LEU 3.4 3.2 + - - +
76B ASN* 3.2 26.5 - - - +
77B ALA* 3.0 29.6 + - - +
253B PHE* 3.7 2.8 - - - +
254B ASP* 1.3 79.1 - - - +
256B LEU* 1.3 62.2 + - - +
257B THR* 4.6 1.0 + - - -
267B HIS* 3.8 22.2 + - - -
268B GLY 3.2 15.0 + - - -
270B ALA* 4.3 3.8 - - - +
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Residues in contact with LEU 256 (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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77B ALA* 3.7 3.8 - - + +
79B LEU* 3.7 33.0 - - + -
250B PHE* 4.0 9.6 - - + -
253B PHE* 4.3 15.5 - - + -
255B SER* 1.3 74.2 + - - +
257B THR* 1.3 72.1 + - - +
258B LEU* 4.4 11.2 - - + -
266B PHE* 3.9 8.7 - - + +
267B HIS* 3.3 5.2 + - - -
268B GLY 2.7 34.7 + - - +
269B PRO 4.3 2.0 - - - +
270B ALA* 3.8 15.9 - - + +
273B ALA* 3.7 15.3 - - + -
294B PHE* 3.7 35.4 - - + -
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Residues in contact with THR 257 (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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39B PHE* 5.5 2.2 - - + -
71B MET* 3.7 11.4 - - + +
76B ASN* 6.1 0.2 - - - +
77B ALA 3.0 14.5 + - - -
78B ILE* 3.3 14.0 - - + -
79B LEU* 2.7 33.8 + - - +
89B LEU* 4.7 7.0 - - + -
255B SER* 4.6 1.2 + - - -
256B LEU* 1.3 73.3 - - - +
258B LEU* 1.3 61.7 + - - +
259B LEU* 3.7 15.9 - - + -
264B LEU* 3.7 23.8 - - + -
266B PHE 3.4 4.0 - - - -
267B HIS* 2.8 27.6 + - - +
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Residues in contact with LEU 258 (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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79B LEU* 3.4 30.1 - - + +
256B LEU* 4.5 12.8 - - + -
257B THR* 1.3 73.4 - - - +
259B LEU* 1.3 60.2 + - - +
264B LEU* 3.5 4.5 - - - +
265B MET* 2.6 46.2 + - + +
266B PHE* 2.8 28.9 + - + +
277B PHE* 3.6 35.9 - - + -
294B PHE* 4.3 15.3 - - + +
295B LEU* 4.2 7.9 - - + -
298B ILE* 4.1 18.8 - - + -
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Residues in contact with LEU 259 (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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64B LEU* 5.1 0.4 - - + -
67B ILE* 3.7 25.1 - - + -
78B ILE* 3.9 7.9 - - + -
79B LEU 3.0 10.2 + - - +
80B GLY* 3.3 5.4 - - - -
81B PRO* 3.2 21.5 - - - +
84B GLY* 3.8 21.5 - - - +
85B GLY 4.2 16.8 - - - +
86B LYS* 4.2 12.6 - - + -
89B LEU* 3.8 18.6 - - + -
257B THR* 3.7 26.2 - - + -
258B LEU* 1.3 74.8 - - - +
260B ALA* 1.3 60.5 + - - +
262B GLY* 4.0 4.9 - - - -
263B ARG 3.5 15.5 - - - +
264B LEU* 4.2 6.7 - - + +
265B MET* 4.5 0.2 - - - -
298B ILE* 3.7 2.4 - - - +
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Residues in contact with ALA 260 (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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81B PRO* 4.3 11.2 - - + -
84B GLY* 4.2 1.5 + - - -
259B LEU* 1.3 78.1 - - - +
261B SER* 1.3 74.2 + - - +
262B GLY 3.2 0.7 - - - -
263B ARG* 3.0 18.6 + - - +
265B MET* 3.7 21.4 - - + +
298B ILE* 4.1 12.6 - - + +
329B ILE* 3.7 28.4 - - + +
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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