Contacts of the helix formed by residues 345 - 355 (chain I) in PDB entry 4K4I
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 GLY 345 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339I SER* 4.1 9.6 - - - -
344I ALA* 1.3 74.9 - - - +
346I THR* 1.3 60.5 + - - -
349I ALA* 2.9 29.3 + - - +
4K T 2.7 31.9 + - - -
5K A 4.2 10.5 - - - -
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Residues in contact with THR 346 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268I SER 4.6 2.5 - - - -
269I VAL* 3.0 27.1 + - - +
270I GLN 3.2 5.9 + - - -
271I GLY* 3.2 30.5 + - - +
339I SER* 4.7 3.3 - - - -
345I GLY* 1.3 71.4 - - - -
347I LYS* 1.3 77.3 + - + +
349I ALA* 3.6 4.6 + - - +
350I GLN* 3.1 32.3 + - - +
4K T 3.5 6.4 + - - +
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Residues in contact with LYS 347 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346I THR* 1.3 92.2 - - + +
348I THR* 1.3 57.8 + - - +
350I GLN* 3.4 14.3 + - - +
351I MET* 2.9 28.8 + - - +
3K G 3.6 54.9 + - + +
4K T 3.1 20.6 + - - +
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Residues in contact with THR 348 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344I ALA* 3.9 7.0 - - + -
345I GLY 3.8 5.4 - - - -
347I LYS* 1.3 73.0 - - - +
349I ALA* 1.3 66.6 + - - +
351I MET* 3.3 15.2 + - + +
352I TRP* 2.9 64.8 + - + +
373I GLN* 4.0 15.0 + - - +
3K G 3.7 6.6 + - - -
4K T 2.6 24.5 + - - -
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Residues in contact with ALA 349 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269I VAL 5.4 0.9 - - - +
335I LEU* 3.7 36.8 - - + +
338I PHE* 3.7 25.3 - - + -
339I SER* 4.3 3.4 - - - +
344I ALA* 5.2 0.2 - - - +
345I GLY 2.9 19.1 + - - +
346I THR* 3.7 9.0 - - - +
348I THR* 1.3 76.7 - - - +
350I GLN* 1.3 57.3 + - - +
352I TRP* 3.3 1.4 + - - -
353I TYR* 3.0 28.4 + - - +
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Residues in contact with GLN 350 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270I GLN* 3.4 35.7 + - - +
335I LEU* 4.0 22.9 - - + +
346I THR* 3.1 28.0 + - - +
347I LYS* 3.7 13.4 + - - +
349I ALA* 1.3 75.2 - - - +
351I MET* 1.3 61.7 + - - +
353I TYR* 3.5 3.4 + - + +
354I GLN* 2.9 30.1 + - - +
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Residues in contact with MET 351 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347I LYS 2.9 17.7 + - - +
348I THR* 3.8 14.4 - - + +
350I GLN* 1.3 74.8 - - - +
352I TRP* 1.3 90.3 + - + +
354I GLN* 3.2 7.7 + - - +
355I GLN* 2.9 43.3 + - + +
368I SER* 4.9 12.3 - - - +
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Residues in contact with TRP 352 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338I PHE* 3.8 22.7 - - + -
341I ILE* 3.9 20.6 - - + -
344I ALA* 3.9 20.2 - - + -
348I THR* 2.9 42.5 + - + +
349I ALA 3.8 2.2 - - - +
351I MET* 1.3 87.9 - - + +
353I TYR* 1.3 64.0 + - - +
355I GLN* 3.0 32.6 + - - +
356I GLY 3.3 0.2 + - - -
357I PHE* 3.1 36.1 + + + -
363I ILE* 3.5 24.2 - - + -
367I ALA* 3.7 12.4 - - + +
368I SER 3.8 13.5 + - - +
369I LEU* 3.8 30.7 - - + -
373I GLN* 3.9 11.2 - - + -
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Residues in contact with TYR 353 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330I GLU* 5.1 1.2 - - - +
331I SER* 3.4 39.8 + - - -
334I VAL* 3.9 22.0 - - + -
335I LEU* 3.9 14.1 - - + -
338I PHE* 4.0 2.6 - - + -
349I ALA 3.0 17.2 + - - +
350I GLN* 3.7 5.6 - - + +
351I MET 3.3 0.2 - - - -
352I TRP* 1.3 75.7 - - - +
354I GLN* 1.3 60.5 + - + +
356I GLY* 2.9 9.7 + - - -
357I PHE 3.9 3.6 - - - +
358I ARG* 2.8 62.5 + - - +
552M PRO 5.7 0.2 - - - +
558M ASP* 3.8 4.3 + - - -
561M ARG* 3.7 37.9 + - - -
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Residues in contact with GLN 354 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350I GLN 2.9 17.6 + - - +
351I MET* 3.2 7.9 + - - +
353I TYR* 1.3 80.7 - - + +
355I GLN* 1.3 72.0 + - - +
356I GLY* 3.1 3.7 + - - -
549M ARG* 5.9 3.0 - - - +
551M LEU* 4.3 15.8 - - - +
552M PRO* 3.5 28.9 - - - +
562M LEU* 6.4 1.8 - - + -
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Residues in contact with GLN 355 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B G 4.8 17.2 - - + +
351I MET* 2.9 37.6 + - + +
352I TRP* 3.0 32.3 + - - +
354I GLN* 1.3 85.0 - - - +
356I GLY* 1.3 59.5 + - - +
357I PHE* 3.5 30.8 + - + -
368I SER* 5.7 4.3 + - - +
549M ARG* 6.3 0.9 - - - +
552M PRO* 3.6 20.0 - - + +
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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