Contacts of the helix formed by residues 270 - 279 (chain A) in PDB entry 3K8G
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 ALA 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ASN* 3.8 22.0 - - - +
58A LEU* 3.6 9.1 - - + +
61A ARG* 4.1 3.1 - - - +
223A ASN* 2.9 25.2 + - + +
224A GLU* 3.7 1.0 - - - +
225A TYR* 3.9 30.3 - - + -
268A ILE 3.7 1.8 + - - -
269A SER* 1.3 70.2 - - - +
271A GLU* 1.3 57.9 + - - +
273A LEU* 4.3 1.3 - - - -
274A ALA* 3.0 31.0 + - - +
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Residues in contact with GLU 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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61A ARG* 3.4 41.9 + - - +
223A ASN 4.7 0.4 + - - -
269A SER* 3.2 9.5 + - - +
270A ALA* 1.3 80.3 - - - +
272A ARG* 1.3 67.0 + - + +
274A ALA* 3.5 2.8 + - - +
275A SER* 3.3 23.4 + - - -
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Residues in contact with ARG 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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200A LYS 2.5 31.1 + - - -
201A LEU* 2.6 25.6 + - - +
202A LEU 5.0 0.4 - - - -
203A ASN* 3.1 42.0 + - - +
267A THR 5.4 1.2 + - - -
268A ILE* 3.6 36.1 - - + +
269A SER* 3.0 19.6 + - - +
271A GLU* 1.3 76.6 - - + +
273A LEU* 1.3 61.6 + - - +
275A SER* 3.3 9.6 + - - +
276A VAL* 2.9 36.7 + - + +
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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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58A LEU* 3.9 21.8 - - + -
189A LEU* 5.8 0.7 - - + -
197A PHE* 5.9 0.9 - - + -
201A LEU* 4.7 7.6 - - + -
216A LEU* 5.3 3.1 - - + -
218A LEU* 3.7 35.0 - - + -
225A TYR* 3.5 36.1 - - + -
268A ILE* 3.7 20.3 - - + +
269A SER 2.9 15.9 + - - +
270A ALA 3.7 4.9 - - - +
272A ARG* 1.3 77.0 - - - +
274A ALA* 1.3 61.9 + - - +
276A VAL* 3.3 6.6 + - + +
277A ILE* 3.0 41.7 + - + +
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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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58A LEU* 3.8 6.4 - - + +
61A ARG* 3.6 30.5 - - + -
62A ILE* 3.8 22.4 - - + +
65A ASN* 3.8 6.7 - - - +
270A ALA 3.0 17.7 + - - +
271A GLU 3.7 4.5 - - - +
272A ARG 3.3 0.2 - - - -
273A LEU* 1.3 76.9 - - - +
275A SER* 1.3 53.0 + - - +
277A ILE* 3.5 2.9 + - - +
278A SER* 2.9 35.2 + - - -
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Residues in contact with SER 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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65A ASN* 4.0 11.8 - - - +
271A GLU* 3.3 15.6 + - - -
272A ARG* 3.5 14.2 - - - +
274A ALA* 1.3 75.3 - - - +
276A VAL* 1.3 60.0 + - - +
278A SER* 3.5 2.2 - - - -
279A SER* 2.8 34.5 + - - -
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Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A PHE* 3.4 37.3 - - + -
200A LYS* 3.9 40.8 + - + +
201A LEU* 4.5 6.5 - - + +
268A ILE* 4.3 12.6 - - + -
272A ARG* 2.9 32.7 + - + +
273A LEU* 3.6 9.0 - - + +
275A SER* 1.3 71.9 - - - +
277A ILE* 1.3 62.2 + - + +
279A SER* 2.8 22.3 + - - -
280A LEU* 3.9 6.4 + - - +
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Residues in contact with ILE 277 (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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48A LEU* 4.1 18.8 - - + -
50A PHE* 4.0 18.4 - - + -
58A LEU* 5.0 0.4 - - + -
62A ILE* 4.0 35.4 - - + -
93A PHE* 3.9 10.8 - - + -
187A VAL* 5.6 0.4 - - + -
189A LEU* 4.5 26.0 - - + -
197A PHE* 4.9 2.5 - - + -
273A LEU* 3.0 38.9 + - + +
274A ALA 3.8 3.4 - - - +
276A VAL* 1.3 77.3 - - + +
278A SER* 1.3 65.3 + - - +
280A LEU* 3.3 29.2 + - + +
300A MPD 6.1 0.2 - - + -
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Residues in contact with SER 278 (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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62A ILE* 4.0 7.4 + - - +
65A ASN* 2.7 43.6 + - - +
66A HIS* 3.2 28.2 + - - -
274A ALA 2.9 16.4 + - - -
275A SER* 3.5 5.4 - - - -
277A ILE* 1.3 76.2 - - - +
279A SER* 1.3 58.2 + - - +
280A LEU 3.0 5.9 + - - -
281A TYR 3.1 19.4 + - - +
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Residues in contact with SER 279 (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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200A LYS* 2.7 34.6 + - - +
275A SER* 2.8 15.9 + - - -
276A VAL* 2.8 19.8 + - - -
278A SER* 1.3 74.8 - - - +
280A LEU* 1.3 63.0 + - - +
281A TYR 3.2 8.0 + - - +
282A SER 4.8 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