Contacts of the helix formed by residues 309 - 324 (chain B) in PDB entry 3GSB
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 ASN 309 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 5.9 0.2 - - - +
278A GLY 5.5 0.7 - - - -
280A PRO* 4.0 21.5 - - - +
91B THR 3.7 10.6 - - - +
92B SER* 4.5 12.3 - - - +
93B PHE 5.5 0.7 - - - +
121B ASN* 4.7 1.8 - - - +
280B PRO 5.0 0.4 + - - -
306B LEU* 3.1 28.8 + - + +
307B SER 3.2 3.7 - - - -
308B GLY* 1.3 76.5 - - - +
310B PRO* 1.3 68.5 - - + +
311B LEU* 3.1 10.6 + - - +
312B ALA* 2.8 43.3 + - - +
313B MET* 2.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA* 5.5 5.2 - - + +
90B GLY 4.2 6.1 - - - +
91B THR 3.2 30.5 - - - +
93B PHE* 4.0 45.3 - - + +
97B CYS* 4.9 8.1 - - - -
99B LEU* 4.2 16.3 - - + +
308B GLY 3.7 2.0 - - - +
309B ASN* 1.3 80.8 - - + +
311B LEU* 1.3 59.3 + - + +
313B MET* 3.1 7.7 + - + +
314B THR* 2.8 34.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 5.3 0.4 - - + -
279A LEU* 4.4 19.1 - - + -
311A LEU* 6.2 2.9 - - + -
83B LEU* 3.3 36.3 - - + +
86B ALA* 4.1 8.7 - - + -
87B MET* 3.4 47.1 - - + +
90B GLY 5.2 0.7 - - - +
91B THR* 4.0 32.1 - - + +
279B LEU* 3.8 15.0 - - + +
309B ASN* 3.1 8.2 + - - +
310B PRO* 1.3 78.3 - - - +
312B ALA* 1.3 62.6 + - - +
314B THR* 3.3 2.3 + - - -
315B ALA* 3.1 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A PRO* 6.0 0.2 - - + -
103B LEU* 5.2 0.3 - - - +
275B ILE 4.5 1.2 - - - +
276B GLY* 4.4 5.5 - - - -
279B LEU* 4.1 15.4 - - + +
280B PRO 4.7 1.6 - - - +
281B VAL* 3.4 30.8 - - + +
308B GLY* 6.2 0.4 - - - +
309B ASN* 2.8 32.9 + - - +
311B LEU* 1.3 73.7 - - - +
313B MET* 1.3 68.4 + - - +
315B ALA* 3.9 1.5 - - - +
316B GLY* 3.0 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 3.7 24.9 - - + +
100B GLU* 3.2 38.4 - - + -
103B LEU* 3.7 21.8 - - + +
119B PHE* 3.3 36.8 - - + -
281B VAL* 6.0 3.6 - - - -
308B GLY* 3.6 19.3 - - - +
309B ASN 2.8 24.5 + - - +
310B PRO* 3.1 4.7 + - + +
312B ALA* 1.3 80.3 - - - +
314B THR* 1.3 62.0 + - - +
316B GLY* 3.8 0.5 - - - -
317B ILE* 3.1 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ALA* 3.6 38.4 - - + +
83B LEU* 4.1 6.5 - - + -
86B ALA* 3.6 18.8 - - + +
99B LEU* 3.6 17.0 - - - +
310B PRO 2.8 22.4 + - - -
311B LEU 3.6 5.6 - - - -
312B ALA 3.2 0.2 - - - -
313B MET* 1.3 78.1 - - - +
315B ALA* 1.3 62.1 + - - +
316B GLY 3.2 0.2 + - - -
317B ILE* 3.9 6.8 - - - +
318B LYS* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL* 4.2 16.3 - - + +
83B LEU* 3.5 30.7 - - + +
276B GLY 3.8 17.5 - - - +
277B GLY* 3.8 8.4 - - - +
279B LEU* 4.4 5.6 - - + -
311B LEU 3.1 10.7 + - - +
312B ALA 4.2 0.9 - - - +
314B THR* 1.3 75.8 - - - +
316B GLY* 1.3 59.2 + - - +
318B LYS* 4.1 3.2 - - - +
319B THR* 2.9 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 4.5 7.0 - - - -
275B ILE 3.1 30.3 - - - -
312B ALA 3.0 13.5 + - - -
313B MET 3.3 2.2 + - - -
314B THR 3.1 0.4 - - - -
315B ALA* 1.3 76.4 - - - +
317B ILE* 1.3 58.8 + - - +
319B THR* 3.3 2.8 + - - -
320B LEU* 3.0 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.1 26.5 - - + +
102B VAL* 3.8 27.4 - - + -
103B LEU* 3.9 21.1 - - + +
106B MET* 3.9 17.7 - - + -
313B MET 3.1 21.0 + - - +
314B THR* 3.9 5.2 - - - +
316B GLY* 1.3 73.8 - - - +
318B LYS* 1.3 59.8 + - + +
320B LEU* 3.2 5.0 + - - +
321B GLU* 2.9 52.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU* 3.5 54.8 + - + +
79B VAL* 4.1 15.5 - - + -
81B GLU* 5.4 4.6 + - - -
82B ALA* 4.2 15.2 - - + +
314B THR 3.2 16.0 + - - +
315B ALA* 4.5 2.2 - - - +
317B ILE* 1.3 75.8 - - + +
319B THR* 1.3 62.4 + - - +
321B GLU* 3.2 29.7 + - + +
322B LEU* 3.1 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO 5.3 2.0 - - - +
71B ILE* 4.5 4.3 - - + -
72B CYS* 4.1 17.5 - - + +
79B VAL* 4.0 12.6 - - - +
274B ILE* 3.7 38.1 - - + +
277B GLY* 3.6 13.4 - - - -
315B ALA 2.9 21.6 + - - -
316B GLY 3.3 4.9 + - - -
317B ILE 3.2 0.2 - - - -
318B LYS* 1.3 78.5 - - - +
320B LEU* 1.3 63.8 + - + +
321B GLU 3.2 0.2 + - - -
322B LEU* 3.2 4.5 + - - +
323B LEU* 3.1 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 4.9 6.7 - - + -
106B MET* 4.6 17.9 - - + +
107B VAL* 4.5 14.1 - - + -
251B PHE* 3.6 44.6 - - + -
255B TYR* 3.7 18.9 + - + +
274B ILE* 4.7 0.7 - - + -
275B ILE* 4.7 12.3 - - + -
316B GLY 3.0 24.9 + - - +
317B ILE* 3.2 5.4 + - - +
319B THR* 1.3 86.1 - - + +
321B GLU* 1.3 62.5 + - - +
323B LEU* 3.4 14.4 + - + +
324B ARG* 3.2 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B MET* 4.6 5.9 - - + +
317B ILE* 2.9 37.7 + - + +
318B LYS* 3.4 33.3 + - + +
320B LEU* 1.3 77.4 - - - +
322B LEU* 1.3 63.7 + - + +
324B ARG* 3.2 38.6 + - - +
325B GLN* 3.4 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B CYS* 3.6 23.8 - - - -
76B HIS* 3.6 42.8 - - + +
78B GLU* 3.9 31.2 - - + +
79B VAL* 4.1 13.2 - - + -
318B LYS* 3.1 19.0 + - + +
319B THR 3.7 1.6 - - - +
321B GLU* 1.3 79.8 - - + +
323B LEU* 1.3 59.2 + - - +
325B GLN* 3.2 31.1 + - + +
328B THR* 3.8 4.2 + - - -
412B LEU* 4.8 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 3.9 24.2 - - + -
72B CYS* 3.9 19.5 - - - -
251B PHE* 4.3 12.1 - - + +
255B TYR* 4.2 6.8 - - + -
274B ILE* 4.2 15.3 - - + -
319B THR* 3.1 32.5 + - + +
320B LEU* 4.0 11.0 - - + +
321B GLU 3.2 0.2 - - - -
322B LEU* 1.3 75.4 - - - +
324B ARG* 1.3 59.3 + - - +
325B GLN 3.2 3.7 - - - +
328B THR* 3.2 36.0 + - + +
329B TYR* 3.6 32.9 - - - +
412B LEU* 4.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B MET* 3.5 36.0 - - - +
255B TYR* 3.1 36.5 + - + +
320B LEU* 3.2 33.0 + - - +
321B GLU* 3.2 25.4 + - - +
323B LEU* 1.3 76.4 - - - +
325B GLN* 1.3 66.5 + - - +
326B PRO* 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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