Contacts of the helix formed by residues 302 - 312 (chain A) in PDB entry 6KW5
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 ASP 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A THR* 3.6 6.2 - - - +
296A GLU* 4.4 0.7 - - - -
300A VAL 5.1 0.3 - - - +
301A VAL* 1.3 84.2 - - - +
303A SER* 1.3 62.0 + - - +
304A THR* 3.9 20.4 + - + +
305A THR* 3.3 12.8 + - - +
306A ARG* 3.3 23.2 + - - +
212M ALA* 3.3 29.3 - - - +
213M THR* 3.6 13.9 + - - -
216M ASN* 2.8 42.0 + - - +
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Residues in contact with SER 303 (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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279A THR* 4.0 16.6 - - - +
281A TRP* 4.8 8.2 + - - +
294A PHE* 3.5 44.3 - - - -
296A GLU* 4.1 5.3 + - - -
302A ASP* 1.3 74.6 - - - +
304A THR* 1.3 63.6 + - - +
306A ARG* 3.9 0.7 - - - +
307A GLY* 2.9 25.5 + - - -
16I ALA* 5.2 6.5 - - - +
17I TYR* 3.6 19.8 + - - -
407I LEU* 5.2 1.6 - - - +
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Residues in contact with THR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ASP* 4.0 11.4 + - + +
303A SER* 1.3 86.5 - - - +
305A THR* 1.3 74.2 + - - +
307A GLY* 3.3 2.3 + - - -
308A LEU* 2.9 33.6 + - - +
16I ALA* 5.6 2.0 - - + -
17I TYR* 4.3 23.1 - - + +
407I LEU* 4.5 7.1 - - - +
410I ASN* 4.9 19.0 - - - +
414I GLN* 4.0 16.7 + - - +
212M ALA* 5.9 0.7 - - - +
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Residues in contact with THR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A VAL* 3.4 13.3 - - - +
302A ASP* 3.3 29.8 + - - +
304A THR* 1.3 88.6 + - - +
306A ARG* 1.3 60.0 + - - +
308A LEU* 3.2 10.2 + - + +
309A ILE* 2.9 39.1 + - - +
27E PHE* 4.7 6.9 - - + -
414I GLN* 4.8 12.1 - - - +
209M GLU* 5.9 3.4 - - - +
212M ALA* 6.3 0.9 - - + -
213M THR* 6.4 1.3 - - - -
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Residues in contact with ARG 306 (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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278A THR* 2.5 40.9 + - - +
279A THR* 3.9 17.6 + - - +
281A TRP* 3.5 35.0 - - + -
301A VAL* 4.2 8.7 - - + -
302A ASP 3.3 18.9 + - - +
303A SER 4.0 2.2 - - - +
304A THR 3.3 0.4 - - - -
305A THR* 1.3 79.9 + - - +
307A GLY* 1.3 58.3 + - - +
309A ILE* 3.3 11.3 + - - +
310A TRP* 2.9 36.6 + - - +
17E ASN 3.4 23.2 + - - -
18E ASN* 6.0 0.6 - - - +
19E VAL* 4.6 22.5 - - - +
11I THR 5.2 1.4 + - - -
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Residues in contact with GLY 307 (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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281A TRP* 4.2 9.8 - - - -
303A SER 2.9 17.7 + - - -
304A THR 3.7 2.7 - - - -
306A ARG* 1.3 77.4 - - - +
308A LEU* 1.3 55.7 + - - +
310A TRP* 3.4 6.5 + - - +
311A LEU* 2.9 26.9 + - - +
13I PRO* 4.7 2.0 - - - -
407I LEU* 3.4 30.2 - - - +
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Residues in contact with LEU 308 (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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304A THR 2.9 19.1 + - - +
305A THR* 3.2 13.9 + - + +
307A GLY* 1.3 73.5 - - - +
309A ILE* 1.3 62.0 + - - +
311A LEU* 3.4 13.6 - - + +
312A GLU* 3.0 36.0 + - + +
27E PHE* 4.3 18.0 - - + -
407I LEU* 3.4 27.4 - - + +
410I ASN* 4.8 5.2 - - + -
411I SER* 3.7 25.8 - - - +
414I GLN* 3.4 33.4 - - - +
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Residues in contact with ILE 309 (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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301A VAL* 5.4 1.8 - - + -
305A THR* 2.9 27.1 + - - +
306A ARG* 3.3 13.9 + - - +
308A LEU* 1.3 76.1 - - - +
310A TRP* 1.3 63.4 + - - +
311A LEU 3.5 0.2 + - - -
312A GLU* 3.7 2.3 + - - +
313A ARG* 3.7 37.9 + - - +
19E VAL* 4.2 22.4 - - + -
23E ASN* 6.2 1.3 - - + -
24E LEU* 3.7 31.0 - - + -
27E PHE* 3.6 41.7 - - + -
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Residues in contact with TRP 310 (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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281A TRP* 4.7 7.4 - + + -
306A ARG* 2.9 24.3 + - - +
307A GLY* 3.6 4.9 - - - +
309A ILE* 1.3 79.8 - - - +
311A LEU* 1.3 67.9 + - + +
313A ARG* 3.6 2.0 + - - +
314A ILE* 3.3 57.6 + - + +
11I THR 4.8 7.0 + - - -
12I TYR* 4.2 16.6 - - + +
13I PRO* 3.5 40.7 - - + +
400I ARG* 5.0 18.4 - - + -
403I THR* 5.7 1.6 - - + -
404I LYS* 4.8 23.6 - - + -
407I LEU* 4.0 15.9 - - + -
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Residues in contact with LEU 311 (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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307A GLY 2.9 18.4 + - - +
308A LEU* 3.1 15.7 + - + +
310A TRP* 1.3 84.6 - - + +
312A GLU* 1.3 64.8 + - + +
313A ARG 3.2 1.3 + - - -
314A ILE 3.1 28.7 - - - +
404I LYS* 3.7 35.9 - - + +
407I LEU* 4.0 16.6 - - + +
408I GLN* 3.8 40.4 - - + +
411I SER* 5.0 4.0 - - - -
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Residues in contact with GLU 312 (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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308A LEU* 3.0 17.1 + - + +
309A ILE 3.7 3.3 + - - +
310A TRP 3.5 0.2 - - - -
311A LEU* 1.3 84.3 - - + +
313A ARG* 1.3 57.8 + - - +
314A ILE 5.0 0.7 - - - -
27E PHE* 3.2 32.4 - - + -
30E LEU* 5.2 9.4 - - - +
31E SER* 5.9 2.0 - - - -
411I SER* 4.8 9.4 + - - -
415I LYS* 5.3 6.8 + - - -
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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