Contacts of the helix formed by residues 299 - 310 (chain I) in PDB entry 5G04
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 299 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290I PHE* 5.6 0.2 - - - -
291I VAL* 5.4 11.7 - - - -
297I THR 4.3 0.2 + - - -
298I THR* 1.3 74.0 - - - +
300I VAL* 1.3 62.8 + - - +
301I GLN* 3.3 3.8 - - - -
302I ASP* 3.3 21.4 + - - +
303I GLU* 3.0 33.0 + - - +
456I PHE 5.8 1.3 - - - -
58O ARG* 4.1 7.6 - - - +
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Residues in contact with VAL 300 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287I LEU* 3.8 31.9 - - + +
290I PHE* 3.5 34.1 - - + -
291I VAL* 4.0 20.7 - - + +
299I SER* 1.3 70.6 - - - +
301I GLN* 1.3 67.6 + - - +
303I GLU* 4.9 2.7 - - - -
304I PHE* 2.9 38.1 + - + +
456I PHE* 3.9 32.0 - - + +
470I PHE* 4.6 8.5 - - + -
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Residues in contact with GLN 301 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299I SER* 3.3 1.9 - - - -
300I VAL* 1.3 80.6 - - - +
302I ASP* 1.3 75.8 + - - +
304I PHE* 3.8 2.1 - - - +
305I MET* 3.0 33.4 + - + +
452I LEU* 3.6 20.9 - - - +
453I THR* 3.8 29.4 + - - +
456I PHE* 3.6 26.0 + - + +
457I ASN* 3.4 29.8 + - - +
62O GLN* 3.5 21.3 + - - +
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Residues in contact with ASP 302 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298I THR* 6.0 0.2 - - - -
299I SER* 3.3 28.2 + - - +
301I GLN* 1.3 92.6 - - - +
303I GLU* 1.3 62.5 + - + +
305I MET* 3.6 7.2 + - - +
306I HIS* 3.3 21.1 + - - +
55O MET* 5.7 1.1 - - - +
58O ARG* 3.5 48.4 + - + +
61O ASN* 5.2 1.7 + - - -
62O GLN* 3.5 20.1 - - - +
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Residues in contact with GLU 303 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290I PHE* 3.3 33.7 - - - -
295I ASN* 5.7 0.5 - - - +
298I THR* 3.5 38.7 - - - +
299I SER 3.0 13.4 + - - +
300I VAL* 4.5 2.0 - - - +
302I ASP* 1.3 73.9 - - - +
304I PHE* 1.3 66.1 + - - +
306I HIS* 3.6 8.1 + - - +
307I LEU 3.3 13.0 + - - -
313I ALA 4.7 2.1 - - - +
314I SER* 4.7 10.8 + - - +
316I GLU* 3.6 20.6 - - - +
317I LEU* 3.4 32.1 - - + +
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Residues in contact with PHE 304 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287I LEU* 4.6 10.1 - - + -
290I PHE* 5.8 1.3 - + - -
300I VAL* 2.9 36.4 + - + +
301I GLN 3.8 0.4 - - - +
303I GLU* 1.3 78.4 - - - +
305I MET* 1.3 51.7 + - - +
307I LEU* 2.7 42.4 + - + +
308I LEU* 2.7 16.5 + - - +
317I LEU* 4.4 19.1 - - + -
320I LEU* 6.0 3.6 - - + -
321I LEU* 5.1 13.7 - - + -
417I PHE* 4.8 10.5 - + - -
420I TRP* 3.8 30.0 - + - -
421I LEU* 4.6 11.9 - - + -
452I LEU* 3.7 19.1 - - + -
456I PHE* 3.9 22.4 - + - -
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Residues in contact with MET 305 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301I GLN* 3.0 22.1 + - + +
302I ASP* 3.8 6.1 - - - +
303I GLU 3.3 0.4 - - - -
304I PHE* 1.3 74.7 - - - +
306I HIS* 1.3 57.6 + - - +
308I LEU* 3.2 17.8 + - - +
309I LEU* 3.0 56.5 + - + +
449I ALA* 4.8 12.6 - - - +
452I LEU* 3.8 18.4 - - + +
453I THR* 5.4 2.7 - - - +
61O ASN* 3.4 27.8 - - + +
62O GLN* 3.2 47.3 - - + +
65O LEU* 4.9 6.7 - - + -
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Residues in contact with HIS 306 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302I ASP 3.3 11.9 + - - +
303I GLU* 3.6 11.4 - - - +
305I MET* 1.3 77.7 - - - +
307I LEU* 1.3 49.1 + - - +
309I LEU 4.7 0.2 - - - +
310I TRP* 2.8 54.5 + + + +
312I LYS* 3.6 37.4 + - + +
313I ALA* 3.8 12.9 + - - -
314I SER* 4.1 12.0 + - - -
57O ARG* 3.9 27.2 + - + -
61O ASN* 3.5 26.3 - - - +
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Residues in contact with LEU 307 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303I GLU 3.3 7.4 + - - +
304I PHE* 2.7 42.0 + - + +
306I HIS* 1.3 73.2 + - - +
308I LEU* 1.3 59.6 + - - +
310I TRP 3.0 19.0 - - - +
311I GLY* 4.8 5.5 - - - +
313I ALA* 3.6 31.2 - - + +
317I LEU* 4.3 10.3 - - + -
321I LEU* 4.7 16.2 - - + -
420I TRP* 3.7 17.4 + - + -
421I LEU* 5.1 2.0 - - + -
424I ALA* 4.1 24.7 - - + -
427I ARG* 5.9 1.1 + - - +
428I MET* 5.8 6.3 - - + -
130O SER* 5.2 0.3 + - - -
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Residues in contact with LEU 308 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304I PHE 2.7 12.4 + - - +
305I MET* 3.2 14.8 + - - +
307I LEU* 1.3 75.0 - - - +
309I LEU* 1.3 74.0 + - + +
420I TRP* 3.6 31.3 + - + +
445I ILE* 4.1 33.8 - - + +
448I VAL* 3.9 14.4 - - + -
449I ALA* 3.8 27.1 - - - +
452I LEU* 3.8 23.6 - - + -
65O LEU* 5.0 1.3 - - + -
130O SER* 4.2 9.9 - - - -
131O VAL* 4.6 6.2 + - + +
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Residues in contact with LEU 309 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305I MET* 3.0 37.0 + - + +
308I LEU* 1.3 96.2 - - + +
310I TRP* 1.3 71.7 + - + +
61O ASN* 3.1 41.5 - - + +
64O LEU* 3.8 23.1 - - + -
65O LEU* 4.2 21.8 - - + -
130O SER* 3.1 17.5 - - - -
131O VAL* 4.8 8.1 - - + -
132O VAL* 3.6 21.9 + - + +
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Residues in contact with TRP 310 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306I HIS* 2.8 44.3 + + + +
307I LEU* 3.0 17.2 - - - +
309I LEU* 1.3 88.6 - - + +
311I GLY* 1.3 58.8 + - - +
312I LYS* 3.0 32.6 + - + +
313I ALA 3.7 0.3 + - - -
41O LEU* 4.9 3.8 - - + -
44O MET* 3.6 31.0 - - + -
45O SER* 4.2 18.5 - - - -
61O ASN* 3.4 32.1 - - - -
64O LEU* 3.7 17.3 - - + -
126O VAL* 4.0 30.4 - - + +
127O HIS* 4.5 4.7 - - - -
130O SER* 3.5 3.4 - - - -
132O VAL* 3.5 33.3 - - + +
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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