Contacts of the helix formed by residues 309 - 318 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86I ILE* 3.6 19.0 - - + +
101I ILE* 3.6 21.3 - - + -
288I ILE* 3.7 22.0 - - + -
290I ILE* 3.4 39.3 - - + -
306I GLN* 4.3 9.9 + - - +
307I SER 2.7 4.2 + - - -
308I LYS* 1.3 80.0 - - + +
310I PHE* 1.3 74.1 + - - +
312I ASN* 3.3 3.1 + - - +
313I THR* 3.0 36.3 + - - -
333I LEU* 3.7 26.0 - - + -
423I LEU* 3.9 26.2 - - + -
426I TYR* 4.2 9.0 - + - -
428I MET* 5.6 0.4 - - - -
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Residues in contact with PHE 310 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A PHE* 6.2 4.3 - + - -
328A LYS* 6.0 1.6 - - - -
330A ARG* 3.3 38.4 - - - -
310E PHE* 6.3 3.1 - + - -
306I GLN 5.1 0.8 + - - +
307I SER* 2.7 29.8 + - - +
309I PHE* 1.3 84.1 - - - +
311I GLU* 1.3 52.3 + - - +
312I ASN 2.6 14.6 + - - -
313I THR* 3.2 8.6 + - - -
314I VAL* 3.5 18.4 + - + +
328I LYS* 4.6 14.8 - - + -
330I ARG* 6.1 3.8 - - - -
333I LEU* 4.0 15.3 - - + -
426I TYR* 3.0 43.7 - + - +
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Residues in contact with GLU 311 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ARG* 3.0 57.5 - - + +
331A LYS* 5.2 4.7 + - - +
333A LEU* 5.7 1.0 - - - +
334A TYR* 3.4 37.2 + - - +
426A TYR* 3.8 21.9 - - - +
307I SER* 2.6 35.3 + - - +
308I LYS* 3.9 4.1 - - - +
310I PHE* 1.3 69.4 - - - +
312I ASN* 1.3 62.9 + - - +
314I VAL* 4.8 2.0 - - - -
315I ALA* 4.4 10.4 - - - +
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Residues in contact with ASN 312 (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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59I ASN* 5.5 3.9 + - - +
78I ALA* 3.4 28.2 - - - +
86I ILE* 4.6 5.2 - - - -
88I PHE* 3.4 26.1 - - + -
308I LYS* 2.7 35.9 + - - +
309I PHE* 3.4 5.4 - - - +
310I PHE 2.6 9.1 + - - -
311I GLU* 1.3 73.0 + - - +
313I THR* 1.3 58.7 + - - +
314I VAL 2.9 4.0 - - - +
315I ALA* 3.5 11.2 - - - +
316I ASP* 2.8 28.6 + - - +
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Residues in contact with THR 313 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88I PHE* 4.1 16.8 - - + -
99I PHE* 3.4 40.8 - - + -
288I ILE* 5.1 0.9 - - + -
309I PHE* 3.0 39.2 + - - -
310I PHE 4.0 3.8 - - - -
312I ASN* 1.3 77.1 + - - +
314I VAL* 1.3 56.2 + - + +
316I ASP* 3.4 2.9 + - - +
317I ILE* 2.7 41.4 + - + +
332I ALA* 5.6 0.7 - - + -
333I LEU* 4.3 15.7 - - + -
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Residues in contact with VAL 314 (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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328A LYS* 6.0 3.1 - - + -
330A ARG* 3.6 34.3 - - + +
310I PHE* 3.5 21.8 - - + +
311I GLU* 4.8 0.4 - - - -
312I ASN 4.5 1.8 - - - +
313I THR* 1.3 77.0 - - - +
315I ALA* 1.3 56.4 + - - +
316I ASP 2.7 14.4 + - - -
317I ILE* 2.7 25.6 + - + -
318I MET* 2.8 15.0 + - + +
326I GLU 5.1 11.0 - - - +
328I LYS* 5.8 2.2 - - + +
333I LEU* 6.4 1.6 - - + -
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Residues in contact with ALA 315 (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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330A ARG* 6.6 0.2 - - + -
331A LYS* 3.5 28.7 - - - +
59I ASN* 5.7 1.9 + - - -
63I ILE* 5.5 6.6 - - - +
311I GLU 4.4 4.5 - - - +
312I ASN* 3.3 20.7 + - - +
314I VAL* 1.3 79.4 - - - +
316I ASP* 1.3 57.0 + - - +
318I MET* 3.7 20.6 - - - +
319I SER* 4.5 6.2 + - - -
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Residues in contact with ASP 316 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I ASN* 3.5 14.8 + - - +
70I LEU* 4.2 21.8 - - - +
76I VAL* 3.5 27.3 - - - +
88I PHE* 4.0 27.0 - - + +
90I ILE* 5.0 4.3 - - - +
95I LEU* 5.5 7.6 - - - +
312I ASN* 2.8 18.6 + - - +
313I THR* 3.5 7.2 - - - +
314I VAL 2.7 1.2 + - - -
315I ALA* 1.3 78.8 - - - +
317I ILE* 1.3 64.1 + - - +
318I MET 3.0 1.6 - - - -
319I SER* 3.1 21.9 + - - -
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Residues in contact with ILE 317 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95I LEU* 3.9 34.4 - - + +
96I TYR 5.3 0.2 - - - +
99I PHE* 4.8 0.4 - - + -
313I THR* 2.7 35.2 + - + +
314I VAL* 2.7 16.6 + - + +
316I ASP* 1.3 73.2 - - - +
318I MET* 1.3 64.4 + - - +
319I SER 3.3 7.0 + - - +
325I ASP* 3.3 31.2 - - + +
326I GLU* 4.5 9.9 - - - +
328I LYS 5.7 0.4 - - - +
329I LEU* 4.4 17.7 - - + -
332I ALA* 3.8 28.3 - - + -
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Residues in contact with MET 318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I ILE* 4.6 17.3 - - + -
65I ALA* 5.2 10.5 - - + -
314I VAL* 2.8 14.4 + - + +
315I ALA* 3.7 14.1 - - - +
317I ILE* 1.3 78.3 - - - +
319I SER* 1.3 74.1 + - - +
325I ASP* 2.8 28.4 - - - +
326I GLU* 5.7 5.4 - - + +
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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