Contacts of the helix formed by residues 304 - 316 (chain B) in PDB entry 6B3I
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 304 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A LYS 5.7 0.2 + - - -
303B THR* 1.3 78.9 - - - +
305B GLY* 1.3 68.1 + - - +
306B ASP* 5.0 0.2 - - - +
307B PHE* 3.7 9.2 + - - +
308B ARG* 3.1 32.8 + - - +
402B EDO 4.3 14.0 + - - -
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Residues in contact with GLY 305 (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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69A LYS 4.0 8.1 - - - -
70A SER* 3.7 28.0 - - - -
304B SER* 1.3 75.5 - - - +
306B ASP* 1.3 67.7 + - - -
307B PHE 4.2 0.2 - - - -
308B ARG* 3.2 16.4 + - - +
309B LYS* 3.2 11.5 + - - +
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Residues in contact with ASP 306 (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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70A SER 3.2 9.7 + - - +
71A GLU 3.0 25.9 - - - +
72A LEU 4.3 4.7 - - - +
73A SER* 4.3 12.7 + - - -
34B GLU* 3.5 23.7 - - - +
38B ILE* 5.1 2.2 - - + -
76B PHE* 3.3 47.3 - - + +
305B GLY* 1.3 73.5 - - - -
307B PHE* 1.3 71.5 + - - +
309B LYS* 3.3 11.3 + - + +
310B LEU 3.0 18.5 + - - -
402B EDO 5.5 1.0 - - - -
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Residues in contact with PHE 307 (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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75B ASN* 3.3 23.8 - - + -
76B PHE* 4.0 13.5 - - - +
79B THR* 3.2 23.6 - - + -
265B GLU* 3.2 39.3 - - + -
268B LEU* 4.8 1.3 - - + -
269B ILE* 3.7 22.4 - - + -
303B THR* 3.8 21.5 - - + -
304B SER 3.8 5.8 - - - +
305B GLY 3.1 0.4 - - - -
306B ASP* 1.3 84.3 + - - +
308B ARG* 1.3 62.9 + - - +
310B LEU* 3.3 3.6 + - + +
311B LEU* 3.2 44.4 + - + +
402B EDO 3.8 23.1 - - - -
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Residues in contact with ARG 308 (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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299B VAL* 4.7 2.0 - - - -
300B ARG* 3.6 31.4 + - - +
303B THR* 2.7 48.9 + - - +
304B SER* 3.1 39.8 + - - +
305B GLY 3.2 4.7 + - - +
307B PHE* 1.3 76.0 - - - +
309B LYS* 1.3 64.9 + - - +
311B LEU* 3.3 1.6 + - - +
312B VAL* 3.0 43.0 + - + +
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Residues in contact with LYS 309 (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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31B GLY* 4.5 9.5 + - - -
34B GLU* 6.2 1.5 - - + +
35B ALA* 4.2 25.1 - - - +
38B ILE* 3.7 21.7 - - + +
305B GLY 3.2 9.3 + - - +
306B ASP* 3.6 13.0 - - - +
307B PHE 3.3 0.2 - - - -
308B ARG* 1.3 81.2 - - - +
310B LEU* 1.3 62.7 + - - +
312B VAL* 4.1 5.2 - - - +
313B ALA* 3.3 21.7 + - - +
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Residues in contact with LEU 310 (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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38B ILE* 3.7 34.3 - - + +
41B LEU* 4.5 8.7 - - + -
42B SER* 4.5 3.1 - - - -
76B PHE* 4.0 31.6 - - + +
79B THR* 3.6 37.5 - - + -
80B ALA* 4.2 9.2 - - - +
83B LEU* 4.5 10.5 - - + -
306B ASP 3.0 15.5 + - - +
307B PHE* 3.8 4.7 - - - +
308B ARG 3.2 0.2 - - - -
309B LYS* 1.3 75.9 - - - +
311B LEU* 1.3 65.4 + - - +
313B ALA* 3.2 2.6 + - - +
314B LEU* 3.0 36.0 + - + +
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Residues in contact with LEU 311 (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 THR* 4.2 11.0 - - + +
268B LEU* 3.7 28.7 - - + -
269B ILE* 5.0 6.3 - - + -
272B ILE* 4.1 22.2 - - + -
273B VAL* 6.2 0.2 - - + -
299B VAL* 3.8 23.6 - - + -
303B THR* 4.6 1.1 - - + -
307B PHE* 3.2 55.7 + - + +
308B ARG 3.3 0.2 + - - -
310B LEU* 1.3 73.0 - - - +
312B VAL* 1.3 66.4 + - - +
314B LEU* 3.0 22.7 + - + +
315B LEU* 3.0 28.7 + - - +
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Residues in contact with VAL 312 (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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296B SER* 3.8 13.5 - - - +
299B VAL* 4.1 12.8 - - + -
300B ARG* 3.5 47.1 - - + +
308B ARG* 3.0 33.1 + - + +
309B LYS* 4.1 5.4 - - - +
311B LEU* 1.3 74.6 - - - +
313B ALA* 1.3 62.1 + - - +
315B LEU* 3.3 6.4 + - - +
316B HIS* 3.1 22.4 + - - +
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Residues in contact with ALA 313 (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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38B ILE* 3.6 13.5 - - + -
42B SER* 3.4 25.2 - - - +
309B LYS 3.3 12.9 + - - +
310B LEU 3.2 8.9 + - - +
311B LEU 3.2 0.6 - - - -
312B VAL* 1.3 81.6 - - - +
314B LEU* 1.3 60.2 + - - +
316B HIS* 3.2 29.5 + - - +
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Residues in contact with LEU 314 (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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41B LEU 4.3 1.1 - - - +
42B SER* 3.8 23.3 - - - +
49B ARG* 6.1 0.4 - - - +
79B THR* 4.0 19.3 - - + -
83B LEU* 3.8 45.1 - - + -
272B ILE* 4.1 20.2 - - + -
273B VAL* 4.9 1.8 - - + -
276B ALA* 6.2 3.4 - - + -
280B LEU* 3.9 16.5 - - - +
281B GLN* 5.5 0.7 + - - -
310B LEU* 3.0 20.5 + - + +
311B LEU* 3.0 18.5 + - + +
313B ALA* 1.3 76.5 - - - +
315B LEU* 1.3 58.0 + - - +
316B HIS* 3.3 16.3 + - + -
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Residues in contact with LEU 315 (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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272B ILE* 4.3 18.8 - - + -
280B LEU* 4.3 19.3 - - + -
281B GLN* 6.0 0.4 - - - +
284B LYS* 2.7 39.8 + - + +
295B LEU* 3.7 29.4 - - + -
296B SER* 3.7 28.2 - - - +
299B VAL* 3.6 32.3 - - + -
311B LEU 3.0 18.8 + - - +
312B VAL 3.8 4.7 - - - +
313B ALA 3.2 0.4 - - - -
314B LEU* 1.3 80.8 - - - +
316B HIS* 1.3 64.5 + - - +
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Residues in contact with HIS 316 (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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42B SER 3.4 23.1 + - - -
43B GLY* 5.2 1.2 - - - -
281B GLN* 5.3 7.7 + - - +
284B LYS* 4.6 6.6 + - - +
296B SER* 4.5 10.0 + - - -
312B VAL* 3.1 14.9 + - - +
313B ALA* 3.2 18.5 + - - +
314B LEU* 3.3 16.2 + - + -
315B LEU* 1.3 84.8 + - - +
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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