Contacts of the helix formed by residues 254 - 271 (chain C) in PDB entry 1T2K
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 254 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B ARG* 5.6 8.1 - - - +
253C MET* 1.3 84.9 + - - +
255C ALA* 1.3 65.2 + - - +
256C GLU 3.4 1.1 - - - +
257C ARG* 3.8 5.6 + - - +
258C LYS* 3.4 23.9 + - - +
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Residues in contact with ALA 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C LYS* 1.3 77.3 - - - +
256C GLU* 1.3 68.9 + - - +
258C LYS* 3.3 12.8 + - + +
259C ARG* 2.8 52.0 + - - +
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Residues in contact with GLU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C MET* 3.4 32.7 + - - +
255C ALA* 1.3 83.3 + - - +
257C ARG* 1.3 60.7 + - - +
259C ARG* 3.3 29.5 + - - +
260C MET* 3.7 11.9 + - - +
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Residues in contact with ARG 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C MET 5.1 7.2 - - - +
254C LYS 3.8 8.3 + - - +
255C ALA 3.4 0.4 - - - -
256C GLU* 1.3 76.4 - - - +
258C LYS* 1.3 66.1 + - - +
260C MET* 3.1 40.7 + - + +
261C ARG* 3.2 27.8 + - + +
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Residues in contact with LYS 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C LYS 3.4 18.0 + - - +
255C ALA* 3.5 12.6 - - + +
257C ARG* 1.3 77.9 - - - +
259C ARG* 1.3 65.0 + - - +
261C ARG* 3.0 26.6 + - + +
262C ASN* 3.1 11.4 + - - +
18F T 5.4 6.5 + - - -
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Residues in contact with ARG 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ALA* 2.8 41.9 + - - +
256C GLU* 3.3 22.0 + - - +
258C LYS* 1.3 73.2 - - - +
260C MET* 1.3 58.4 + - + +
262C ASN* 2.9 11.8 + - - +
263C ARG* 2.8 30.9 + - - +
10E T 3.7 37.3 + - - +
11E A 5.6 4.2 + - - -
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Residues in contact with MET 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C GLU 3.7 7.5 + - - +
257C ARG* 3.1 41.0 + - + +
259C ARG* 1.3 77.0 - - - +
261C ARG* 1.3 66.8 + - + +
263C ARG* 3.1 40.5 + - - +
264C ILE* 3.0 39.2 + - + +
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Residues in contact with ARG 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PRO* 4.2 30.6 - - - +
257C ARG* 3.5 34.5 - - + +
258C LYS* 3.0 19.6 + - + +
260C MET* 1.3 79.3 - - - +
262C ASN* 1.3 63.4 + - - +
264C ILE* 3.6 12.8 + - - +
265C ALA* 3.2 22.0 + - - +
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Residues in contact with ASN 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C LYS 3.1 7.3 + - - +
259C ARG* 2.9 17.1 + - - +
261C ARG* 1.3 80.9 - - - +
263C ARG* 1.3 56.5 + - - +
265C ALA* 3.3 7.6 + - - +
266C ALA* 2.8 28.7 + - - +
10E T 4.2 18.6 - - + +
11E A 4.7 17.0 + - - +
21F C 4.7 15.0 + - - +
22F T 5.6 0.4 + - - -
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Residues in contact with ARG 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C ARG* 2.8 13.3 + - - +
260C MET* 3.1 55.8 - - - +
262C ASN* 1.3 70.7 - - - +
264C ILE* 1.3 59.2 + - + +
266C ALA* 3.4 7.7 - - - +
267C SER* 2.7 36.1 + - - -
270C ARG* 4.0 1.9 + - - -
9E A 3.9 46.7 + - + +
10E T 4.1 28.9 + - + +
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Residues in contact with ILE 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C MET* 3.0 31.5 + - + +
261C ARG* 3.9 14.1 - - - +
263C ARG* 1.3 80.4 - - + +
265C ALA* 1.3 58.8 + - - +
267C SER* 3.2 7.8 + - - -
268C LYS* 2.9 47.8 + - + +
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Residues in contact with ALA 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C ARG 3.2 14.2 + - - +
262C ASN* 3.6 9.9 - - - +
263C ARG 3.2 0.2 - - - -
264C ILE* 1.3 78.6 - - - +
266C ALA* 1.3 61.3 + - - +
268C LYS* 3.2 17.9 + - + +
269C SER* 2.8 28.6 + - - -
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Residues in contact with ALA 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C ASN* 2.8 18.3 + - - +
263C ARG 3.0 3.3 + - - +
265C ALA* 1.3 77.4 - - - +
267C SER* 1.3 56.7 + - - +
269C SER* 3.0 8.0 + - - -
270C ARG* 2.8 50.2 + - - +
9E A 4.4 0.4 - - - +
10E T 3.8 29.6 - - + +
22F T 5.9 4.7 - - - +
23F A 5.6 1.3 - - - +
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Residues in contact with SER 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C ARG 2.7 20.0 + - - -
264C ILE* 3.5 8.7 - - - -
266C ALA* 1.3 73.0 - - - +
268C LYS* 1.3 56.2 + - - +
270C ARG* 3.1 16.8 + - - +
271C LYS* 2.7 64.0 + - - +
8E C 5.0 6.2 + - - -
9E A 5.7 2.5 - - - -
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Residues in contact with LYS 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C ILE* 2.9 37.5 + - + +
265C ALA* 3.5 14.9 - - + +
266C ALA 3.2 0.2 - - - -
267C SER* 1.3 75.2 - - - +
269C SER* 1.3 59.4 + - - +
271C LYS* 3.8 8.2 - - - +
272C ARG* 2.8 32.5 + - - +
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Residues in contact with SER 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C ALA 2.8 17.9 + - - -
266C ALA* 3.0 7.8 + - - -
268C LYS* 1.3 79.1 - - - +
270C ARG* 1.3 60.5 + - - +
272C ARG* 3.8 4.6 - - - +
273C LYS* 3.0 25.5 + - - +
21F C 5.4 0.3 - - - +
22F T 4.2 30.1 + - - +
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Residues in contact with ARG 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C ARG 4.0 3.2 + - - -
266C ALA* 2.8 30.9 + - - +
267C SER* 3.1 36.0 + - - +
269C SER* 1.3 73.8 - - - +
271C LYS* 1.3 65.0 + - + +
273C LYS* 3.4 10.2 + - + +
274C LEU* 3.3 27.9 + - + +
7E A 4.2 6.8 - - - +
8E C 2.8 79.5 + - - +
9E A 3.8 18.4 + - - +
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Residues in contact with LYS 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C SER* 2.7 45.6 + - - +
268C LYS* 3.8 6.7 - - - +
270C ARG* 1.3 76.3 - - + +
272C ARG* 1.3 64.7 + - - +
274C LEU* 3.1 20.2 + - - +
275C GLU* 3.1 27.4 + - - +
8E C 5.5 4.9 - - - +
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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