Contacts of the helix formed by residues 309 - 318 (chain K) in PDB entry 2GLJ
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 PHE 309 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86K ILE* 3.6 18.8 - - + -
101K ILE* 3.6 20.6 - - + -
288K ILE* 3.7 21.8 - - + -
290K ILE* 3.4 40.2 - - + -
306K GLN* 4.2 11.0 + - - +
307K SER 2.7 4.0 + - - -
308K LYS* 1.3 79.5 - - + +
310K PHE* 1.3 75.2 + - - +
312K ASN* 3.3 3.2 + - - +
313K THR* 3.0 36.4 + - - -
333K LEU* 3.7 26.2 - - + -
423K LEU* 3.9 24.9 - - + -
426K TYR* 4.3 8.7 - + - -
428K MET* 5.7 0.7 - - - -
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Residues in contact with PHE 310 (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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310J PHE* 6.4 1.8 - + - -
306K GLN 5.1 0.6 + - - +
307K SER* 2.7 30.0 + - - +
309K PHE* 1.3 83.3 - - - +
311K GLU* 1.3 51.9 + - - +
312K ASN 2.6 14.7 + - - -
313K THR* 3.2 9.2 + - - -
314K VAL* 3.5 17.9 + - + +
328K LYS* 4.6 13.7 - - + -
330K ARG* 6.1 3.6 - - - -
333K LEU* 3.9 15.0 - - + -
426K TYR* 3.0 44.0 - + - +
310L PHE* 6.1 4.5 - + - -
328L LYS* 5.9 1.6 - - - -
330L ARG* 3.0 42.2 - - - -
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Residues in contact with GLU 311 (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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307K SER* 2.7 32.7 + - - +
308K LYS* 3.9 4.0 - - - +
310K PHE* 1.3 69.4 - - - +
312K ASN* 1.3 63.1 + - - +
314K VAL* 4.8 2.2 - - - -
315K ALA* 4.4 10.2 - - - +
330L ARG* 3.1 57.0 - - + +
331L LYS* 5.0 6.9 + - - +
333L LEU* 5.7 0.7 - - - +
334L TYR* 3.2 38.8 + - - +
426L TYR* 3.8 20.4 - - - +
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Residues in contact with ASN 312 (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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59K ASN* 5.5 4.2 + - - +
78K ALA* 3.4 27.6 - - - +
86K ILE* 4.6 4.5 - - - -
88K PHE* 3.4 26.0 - - + -
308K LYS* 2.7 34.3 + - - +
309K PHE* 3.3 5.4 - - - +
310K PHE 2.6 8.7 + - - -
311K GLU* 1.3 72.5 + - - +
313K THR* 1.3 59.5 + - - +
314K VAL 2.8 3.1 - - - +
315K ALA* 3.5 11.6 - - - +
316K ASP* 2.8 29.6 + - - +
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Residues in contact with THR 313 (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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88K PHE* 4.1 16.8 - - + -
99K PHE* 3.4 40.8 - - + -
288K ILE* 4.7 0.8 - - + +
309K PHE* 3.0 40.0 + - - -
310K PHE 4.0 3.8 - - - -
312K ASN* 1.3 76.5 + - - +
314K VAL* 1.3 54.5 + - - +
316K ASP* 3.5 2.4 + - - +
317K ILE* 2.7 41.3 + - + +
332K ALA* 5.6 0.7 - - + -
333K LEU* 4.4 14.4 - - + -
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Residues in contact with VAL 314 (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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310K PHE* 3.5 20.2 - - + +
311K GLU* 4.8 0.7 - - - -
312K ASN 2.8 2.2 - - - +
313K THR* 1.3 78.8 - - + +
315K ALA* 1.3 56.6 + - - +
316K ASP 2.7 6.9 + - - -
317K ILE* 2.7 33.5 + - + -
318K MET* 2.7 14.3 + - + +
326K GLU 5.1 10.8 - - - +
328K LYS* 5.8 1.8 - - + +
333K LEU* 6.4 1.1 - - + -
328L LYS* 5.9 3.8 - - + -
330L ARG* 3.6 35.7 - - + +
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Residues in contact with ALA 315 (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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59K ASN* 5.7 1.2 + - - -
63K ILE* 5.6 5.9 - - - +
311K GLU 4.4 4.0 - - - +
312K ASN* 3.2 22.3 + - - +
314K VAL* 1.3 79.4 - - - +
316K ASP* 1.3 57.3 + - - +
318K MET* 3.7 20.1 - - - +
319K SER* 4.4 6.1 + - - -
331L LYS* 3.3 30.3 - - - +
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Residues in contact with ASP 316 (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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59K ASN* 3.5 25.2 + - - +
70K LEU* 4.2 21.7 - - - +
76K VAL* 3.5 16.4 - - - +
88K PHE* 4.0 28.5 - - + +
90K ILE* 5.0 4.3 - - - +
95K LEU* 5.5 8.0 - - - +
312K ASN* 2.8 18.3 + - - +
313K THR* 3.5 7.2 - - - +
314K VAL 2.7 1.4 + - - -
315K ALA* 1.3 77.9 - - - +
317K ILE* 1.3 63.6 + - - +
318K MET 3.0 1.6 - - - -
319K SER* 3.1 21.8 + - - -
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Residues in contact with ILE 317 (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 LEU* 3.9 35.7 - - + +
96K TYR 5.3 0.7 - - - +
99K PHE* 4.9 0.2 - - + -
313K THR* 2.7 31.4 + - + +
314K VAL* 2.7 19.6 + - + +
316K ASP* 1.3 72.5 + - - +
318K MET* 1.3 63.5 - - - +
319K SER 3.3 7.0 + - - +
325K ASP* 3.3 31.1 - - + +
326K GLU 4.6 9.6 - - - +
328K LYS 5.7 0.7 - - - +
329K LEU* 4.4 18.2 - - + -
332K ALA* 3.8 28.5 - - + -
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Residues in contact with MET 318 (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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63K ILE* 4.6 16.8 - - + -
65K ALA* 5.2 10.8 - - + +
314K VAL* 2.7 14.4 + - + +
315K ALA* 3.7 15.5 - - - +
317K ILE* 1.3 78.5 - - - +
319K SER* 1.3 73.8 + - - +
325K ASP* 2.8 27.8 - - - +
326K GLU* 5.7 5.2 - - + +
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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