Contacts of the helix formed by residues 331 - 340 (chain E) in PDB entry 4K4G
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 331 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270E GLN* 4.7 3.1 + - - -
329E SER* 2.9 20.8 + - - -
330E GLU* 1.3 79.8 - - - +
332E VAL* 1.3 67.0 + - - +
333E PRO 3.3 0.4 - - - -
334E VAL* 3.1 7.2 + - - +
335E LEU* 2.9 37.2 + - - +
353E TYR* 3.5 39.6 + - - -
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Residues in contact with VAL 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E ALA* 3.9 34.5 - - + +
269E VAL* 4.2 8.1 - - + +
270E GLN* 4.0 21.5 - - + +
328E ILE* 3.4 33.4 - - + -
329E SER* 3.2 4.8 + - - +
330E GLU 3.2 0.6 - - - -
331E SER* 1.3 78.5 + - - +
333E PRO* 1.3 74.9 - - + +
335E LEU* 3.0 8.8 + - - +
336E GLU* 3.0 36.6 + - + +
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Residues in contact with PRO 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328E ILE* 5.5 0.7 - - + -
329E SER 3.9 3.8 - - - +
330E GLU* 3.3 17.9 - - - +
331E SER 3.4 0.2 - - - -
332E VAL* 1.3 98.8 - - + +
334E VAL* 1.3 59.0 + - + +
336E GLU* 3.4 17.6 - - + +
337E LEU* 3.0 25.8 + - - +
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Residues in contact with VAL 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E GLU 4.7 8.3 - - - +
331E SER 3.1 8.6 + - - +
333E PRO* 1.3 76.7 - - + +
335E LEU* 1.3 67.4 + - - +
337E LEU* 3.3 8.3 + - + +
338E PHE* 3.0 53.7 + - + -
353E TYR* 3.9 19.3 - - + -
358E ARG* 3.8 38.4 - - - +
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Residues in contact with LEU 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E VAL* 4.0 30.4 - - + +
270E GLN* 4.2 18.2 - - + -
331E SER* 2.9 37.1 + - - +
332E VAL* 3.6 5.4 - - - +
334E VAL* 1.3 77.3 - - - +
336E GLU* 1.3 55.1 + - - +
338E PHE* 3.4 1.0 + - + -
339E SER* 2.9 31.6 + - - -
349E ALA* 3.6 40.4 - - + +
350E GLN* 3.8 18.8 - - + +
353E TYR* 3.8 20.0 - - + -
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Residues in contact with GLU 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E LYS* 4.0 26.6 - - + +
269E VAL* 4.0 17.7 - - + -
332E VAL* 3.0 28.9 + - + +
333E PRO* 3.4 21.3 - - - +
334E VAL 3.2 0.2 - - - -
335E LEU* 1.3 73.1 - - - +
337E LEU* 1.3 69.1 + - - +
339E SER* 3.3 6.8 + - - -
340E ASN* 2.9 38.0 + - - +
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Residues in contact with LEU 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333E PRO 3.0 11.1 + - - +
334E VAL* 3.4 11.9 - - + +
336E GLU* 1.3 82.4 - - - +
338E PHE* 1.3 70.5 + - + +
340E ASN* 3.3 7.6 - - - +
341E ILE* 4.3 0.7 - - - +
358E ARG 4.0 20.9 - - - +
359E SER* 4.1 14.1 - - - -
360E LEU* 4.1 26.2 - - + +
380E TYR* 3.1 42.8 + - + +
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Residues in contact with PHE 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334E VAL* 3.0 28.5 + - + +
335E LEU* 5.0 0.7 - - - -
337E LEU* 1.3 90.0 - - + +
339E SER* 1.3 57.6 + - - +
341E ILE* 3.0 32.5 + - + +
344E ALA* 3.8 6.9 - - - +
349E ALA* 3.6 33.2 - - + -
352E TRP* 3.8 32.3 - + + -
353E TYR* 4.2 5.8 - - + -
357E PHE 3.5 32.1 - - - -
359E SER 3.7 19.7 - - - -
360E LEU* 4.7 3.1 - - + -
363E ILE* 3.6 30.5 - - + -
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Residues in contact with SER 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E LYS* 4.8 4.0 + - - -
269E VAL* 3.8 13.4 - - - +
335E LEU 2.9 18.7 + - - -
336E GLU* 3.3 8.8 + - - -
338E PHE* 1.3 72.7 - - - +
340E ASN* 1.3 59.2 + - - +
341E ILE 3.0 5.2 - - - -
344E ALA 3.4 15.0 - - - -
345E GLY* 4.2 18.2 - - - -
346E THR* 4.8 4.7 - - - -
349E ALA* 4.2 2.0 - - - +
606E CA 2.3 28.7 - - - -
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Residues in contact with ASN 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E LYS* 4.5 13.3 + - - -
336E GLU* 2.9 27.6 + - - +
337E LEU* 3.3 12.0 - - - +
339E SER* 1.3 74.4 - - - +
341E ILE* 1.3 59.4 + - - +
342E TRP 3.7 2.1 + - - -
376E GLY 5.5 0.3 - - - +
380E TYR* 3.4 32.2 + - + +
383E PHE* 5.8 3.8 - - - +
384E LEU* 4.1 30.6 - - + +
606E CA 4.4 0.2 - - - -
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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