Contacts of the strand formed by residues 269 - 274 (chain A) in PDB entry 3GG0
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 VAL 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A PHE* 3.7 34.5 - - + -
235A GLN* 5.9 0.4 - - - -
236A LEU* 3.6 9.4 - - + +
238A ILE* 5.2 3.1 - - + -
259A LEU* 3.8 28.9 - - + -
264A LEU* 4.5 11.7 - - + -
265A ARG 3.5 14.8 - - - +
266A PRO 3.0 11.3 + - - +
267A ASP 4.5 1.1 - - - -
268A GLN* 1.3 82.3 - - - +
270A LEU* 1.3 64.9 + - - +
271A ILE* 4.4 17.3 - - + -
297A MET* 3.7 7.2 - - + +
298A LYS* 3.1 22.3 + - - +
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Residues in contact with LEU 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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235A GLN* 4.4 18.4 - - + +
236A LEU 2.7 15.9 + - - +
237A ALA* 3.4 12.2 - - + -
238A ILE* 2.8 31.0 + - - +
269A VAL* 1.3 75.4 - - - +
271A ILE* 1.3 65.6 + - - +
272A GLU* 3.8 15.9 - - + +
298A LYS* 3.3 27.4 - - + +
299A LEU 4.6 1.8 - - - +
300A ALA* 3.5 27.1 - - + -
320A ASP* 5.0 1.1 - - + -
321A LYS* 4.0 40.2 - - + +
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Residues in contact with ILE 271 (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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223A PHE* 5.8 0.2 - - + -
238A ILE* 3.4 22.9 - - + +
240A LEU* 4.1 24.5 - - + -
245A LEU* 4.5 9.2 - - + -
255A LEU* 4.3 24.9 - - + -
269A VAL* 4.4 13.2 - - + -
270A LEU* 1.3 76.5 - - - +
272A GLU* 1.3 59.8 + - - +
273A VAL* 4.5 13.9 - - + -
292A LEU* 4.1 21.8 - - + -
297A MET* 4.4 7.2 - - + -
298A LYS 2.8 17.6 + - - +
299A LEU* 3.6 12.3 - - + +
300A ALA 2.7 33.7 + - - +
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Residues in contact with GLU 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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176A ILE* 5.2 0.2 - - - +
188A GLU* 3.3 13.3 - - - +
237A ALA* 3.4 16.9 - - + +
238A ILE 2.5 17.0 + - - +
239A ASN* 3.4 12.0 - - - +
240A LEU 3.1 25.2 + - - +
270A LEU* 3.8 19.6 - - + +
271A ILE* 1.3 71.2 - - - +
273A VAL* 1.3 60.8 + - - +
274A THR 4.4 0.3 + - - -
300A ALA* 3.6 10.8 - - + -
302A ASP* 3.0 12.0 - - + +
323A LYS* 2.8 31.5 + - + +
502A MN 2.0 37.6 + - - -
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Residues in contact with VAL 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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240A LEU 3.3 20.6 - - - +
242A PRO* 4.6 9.2 - - + -
245A LEU* 4.4 13.7 - - + -
271A ILE* 4.5 7.9 - - + -
272A GLU* 1.3 74.7 - - - +
274A THR* 1.3 59.4 + - - +
278A VAL* 3.6 24.0 - - + -
285A PHE* 4.1 20.6 - - + -
299A LEU* 3.8 17.3 - - + -
300A ALA 3.1 13.6 + - - +
301A ILE* 3.5 10.7 - - + +
302A ASP* 2.6 30.6 + - - -
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Residues in contact with THR 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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240A LEU 4.9 1.2 + - - -
241A LEU* 4.5 12.6 - - + +
242A PRO* 5.1 0.9 - - - +
272A GLU 4.3 0.4 + - - -
273A VAL* 1.3 73.1 - - - +
275A GLU* 1.3 66.2 + - - +
276A THR* 3.2 8.5 - - + -
277A GLU* 3.0 39.8 + - - +
278A VAL* 3.3 13.3 + - - +
302A ASP* 3.6 15.5 - - + +
303A ASP* 4.0 22.2 - - + +
501A C2E 5.2 7.6 - - - +
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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