Contacts of the strand formed by residues 269 - 275 (chain A) in PDB entry 4GLM
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 LYS 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A TYR* 4.0 23.3 + - + -
248A GLY 3.5 4.3 - - - -
249A VAL* 4.2 23.0 - - + +
267A GLY 3.5 9.8 + - - +
268A ASP* 1.3 73.7 - - - +
270A ILE* 1.3 62.0 + - - +
284A SER 4.4 0.3 - - - +
285A LEU* 3.4 17.0 - - - +
298B LYS* 4.8 12.9 - - - +
259C PRO* 5.8 4.3 - - - -
260C ASN* 6.3 4.3 - - - +
257D LEU* 3.8 36.1 - - + +
258D GLU* 4.2 3.6 - - - +
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Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A TYR* 3.1 3.5 - - - -
248A GLY 2.7 46.7 + - - +
250A ALA* 4.4 1.1 - - + -
262A LEU* 3.7 20.9 - - + -
264A PHE* 3.6 39.0 - - + -
268A ASP 4.3 8.1 - - - +
269A LYS* 1.3 75.6 - - - +
271A ARG* 1.4 72.7 + - - +
272A ILE* 3.5 1.1 + - + +
284A SER 3.6 8.7 - - - +
285A LEU* 4.3 13.5 - - + -
292A PHE* 3.7 29.4 - - + -
297A VAL* 3.9 20.4 - - + -
257D LEU* 4.1 2.7 - - - -
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Residues in contact with ARG 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 4.8 17.7 - - - +
246A THR 3.9 9.0 - - - +
247A TYR* 4.5 0.9 - - + +
270A ILE* 1.4 69.3 - - - +
272A ILE* 1.3 69.4 + - - +
273A LEU* 3.5 16.9 + - + +
283A GLY* 3.1 6.9 - - - -
284A SER* 2.9 45.6 + - - +
254D PHE* 3.7 23.2 - - - -
255D GLN* 3.0 31.1 + - - +
257D LEU* 3.6 29.0 - - + +
261D GLU* 3.2 28.1 + - - -
280D TRP* 5.8 2.4 - - - -
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Residues in contact with ILE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A LEU 5.3 2.6 + - - -
246A THR* 2.9 42.9 + - + +
248A GLY* 3.8 12.8 - - - +
270A ILE* 3.8 11.7 - - + +
271A ARG* 1.3 77.3 - - - +
273A LEU* 1.3 64.2 + - - +
274A ALA 4.1 20.2 - - - +
275A THR* 4.8 6.3 - - + -
281A LEU* 4.1 14.8 - - + -
282A GLU 3.9 2.2 - - - +
292A PHE* 3.7 30.5 - - + -
299A LEU* 3.8 28.5 - - + -
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ARG* 4.1 27.4 - - - +
272A ILE* 1.3 78.4 - - - +
274A ALA* 1.4 60.6 + - + +
282A GLU* 2.8 24.3 + - + +
283A GLY* 4.0 12.1 - - - -
284A SER* 4.1 11.7 - - - +
289A THR* 3.7 31.0 - - + +
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ILE* 3.8 4.2 - - - +
273A LEU* 1.4 79.6 - - - +
275A THR* 1.3 64.2 + - - +
276A LEU* 4.5 11.4 - - + -
281A LEU* 3.5 5.5 - - - +
282A GLU* 2.8 47.4 + - + +
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Residues in contact with THR 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ILE* 4.8 7.6 - - + -
274A ALA* 1.3 75.0 - - - +
276A LEU* 1.3 67.1 + - - +
281A LEU* 3.6 25.8 - - + -
299A LEU* 6.0 3.4 - - + -
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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