Contacts of the helix formed by residues 295 - 306 (chain A) in PDB entry 3KGA
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 SER 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A GLU* 5.3 3.3 + - - -
293A GLU 3.9 2.2 + - - -
294A VAL* 1.3 81.4 - - - +
296A GLU* 1.3 64.9 + - - +
297A GLU* 3.3 14.6 + - - +
298A VAL* 3.2 31.2 + - - +
299A LYS* 3.3 12.6 + - - +
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Residues in contact with GLU 296 (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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284A TYR* 4.8 2.3 + - - -
294A VAL 3.9 0.2 + - - -
295A SER* 1.3 74.0 - - - +
297A GLU* 1.3 56.1 + - - +
299A LYS* 3.1 22.9 + - - +
300A MET* 2.9 46.7 + - - +
303A ARG* 2.9 36.1 + - - -
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Residues in contact with GLU 297 (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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295A SER* 3.1 11.7 + - - +
296A GLU* 1.3 78.4 - - - +
298A VAL* 1.3 64.1 + - + +
300A MET* 3.2 14.8 + - - +
301A LEU* 3.1 20.3 + - - +
322A HIS* 3.9 28.6 + - + +
323A PRO* 4.2 17.0 - - - +
324A TRP* 5.0 10.5 - - - -
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Residues in contact with VAL 298 (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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160A GLU* 3.5 12.6 - - - +
253A MET* 3.8 9.2 - - + -
257A LEU* 3.6 31.6 - - + -
294A VAL* 3.6 15.3 - - + -
295A SER* 3.2 19.1 + - - +
297A GLU* 1.3 78.5 - - + +
299A LYS* 1.3 60.4 + - - +
301A LEU* 3.3 10.3 + - - +
302A ILE* 3.1 24.3 + - + +
324A TRP* 3.3 39.7 - - + +
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Residues in contact with LYS 299 (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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284A TYR* 3.9 12.8 + - - +
286A PHE* 3.8 54.8 + - + +
288A ASN* 5.9 0.6 + - - -
291A TRP* 4.0 21.1 + - + +
292A SER* 5.6 1.6 + - - +
294A VAL* 3.8 25.5 + - + -
295A SER 3.3 9.5 + - - +
296A GLU* 3.1 26.8 + - - +
298A VAL* 1.3 74.3 - - - +
300A MET* 1.3 61.3 + - - +
302A ILE* 3.3 4.4 + - - +
303A ARG* 2.9 41.0 + - - +
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Residues in contact with MET 300 (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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296A GLU* 2.9 44.9 + - - +
297A GLU* 3.6 12.1 - - - +
299A LYS* 1.3 73.4 - - - +
301A LEU* 1.3 68.3 + - - +
303A ARG* 3.2 14.4 + - - +
304A ASN* 2.9 33.8 + - - +
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Residues in contact with LEU 301 (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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253A MET* 3.8 27.1 - - + -
297A GLU 3.1 12.5 + - - +
298A VAL* 3.4 9.4 - - - +
300A MET* 1.3 79.5 - - - +
302A ILE* 1.3 62.4 + - - +
304A ASN* 3.1 13.7 + - - +
305A LEU* 3.2 14.2 + - + +
314A MET* 3.5 32.8 - - + -
319A PHE* 4.0 16.8 - - + -
322A HIS* 3.7 42.1 + - + +
324A TRP* 4.0 17.9 - - + -
325A ILE* 4.8 1.3 - - + -
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Residues in contact with ILE 302 (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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250A GLY 4.6 5.8 - - - +
253A MET* 3.6 22.2 - - + -
254A TYR* 4.2 14.1 - - + +
257A LEU* 3.9 15.7 - - + -
286A PHE* 4.1 18.2 - - + -
291A TRP* 3.7 35.4 - - + -
298A VAL* 3.1 16.2 + - + +
299A LYS 3.6 6.5 - - - +
301A LEU* 1.3 72.8 - - - +
303A ARG* 1.3 65.5 + - - +
305A LEU* 3.0 9.5 + - - +
306A LEU* 2.9 46.2 + - + +
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Residues in contact with ARG 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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284A TYR* 3.8 28.5 + - - -
285A GLU* 4.3 11.0 + - + +
286A PHE* 4.0 25.2 - - + -
296A GLU* 2.9 32.5 + - - -
299A LYS* 2.9 21.2 + - - +
300A MET* 3.8 24.4 - - - +
302A ILE* 1.3 74.0 - - - +
304A ASN* 1.3 62.8 + - - +
306A LEU* 3.7 5.6 - - - +
307A LYS* 3.1 29.1 + - + +
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Residues in contact with ASN 304 (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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300A MET* 2.9 31.6 + - - +
301A LEU* 3.4 9.9 - - - +
302A ILE 3.1 0.2 - - - -
303A ARG* 1.3 79.9 - - - +
305A LEU* 1.3 59.4 + - - +
306A LEU 3.6 0.2 + - - -
307A LYS* 3.7 7.8 + - - +
312A GLN 4.6 4.3 - - - +
313A ARG* 3.5 8.5 - - - +
314A MET* 2.9 51.7 + - + +
322A HIS* 6.3 0.8 - - - -
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Residues in contact with LEU 305 (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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246A MET* 3.6 38.8 - - + +
247A TRP* 3.5 14.4 + - - -
249A LEU* 4.3 4.0 - - + -
250A GLY* 3.6 30.1 - - - +
253A MET* 4.0 17.3 - - - -
301A LEU* 3.2 17.6 + - + +
302A ILE* 3.0 7.7 + - - +
304A ASN* 1.3 77.2 - - - +
306A LEU* 1.3 57.9 + - - +
307A LYS 3.3 1.3 - - - -
313A ARG* 3.3 23.4 - - - -
314A MET* 3.6 22.0 - - + -
319A PHE* 3.6 28.3 - - + -
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Residues in contact with LEU 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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247A TRP* 3.8 31.2 - - + +
250A GLY* 3.9 4.3 - - - +
251A VAL* 3.8 32.1 - - + +
254A TYR* 4.7 2.7 - - + -
262A PRO* 3.9 26.9 - - + -
285A GLU* 6.4 2.7 - - + -
286A PHE* 6.0 0.7 - - + -
302A ILE* 2.9 38.3 + - + +
303A ARG* 3.7 6.1 - - - +
305A LEU* 1.3 76.5 - - - +
307A LYS* 1.3 69.3 + - - +
308A THR* 3.2 5.7 + - - -
313A ARG* 4.5 0.7 - - - -
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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