Contacts of the helix formed by residues 312 - 321 (chain D) in PDB entry 4IGM
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 312 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A HIS* 4.6 3.4 - - - -
33A SER* 4.0 15.0 + - - +
36A GLU* 3.6 26.6 - - - +
310D GLU 3.8 2.6 + - - -
311D PHE* 1.3 77.6 - - - +
313D GLU* 1.3 60.6 + - - +
314D GLU* 2.8 23.1 + - - +
315D THR* 2.7 42.3 + - - -
316D LYS* 3.1 26.9 + - - +
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Residues in contact with GLU 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A HIS* 5.6 0.4 + - - -
36A GLU* 4.5 5.9 + - - +
38A LYS* 4.2 24.2 + - - +
48A VAL* 6.2 2.0 - - + -
312D ASP* 1.3 73.5 - - - +
314D GLU* 1.3 60.7 + - - +
316D LYS* 3.9 18.4 + - - +
317D ASN* 3.0 52.6 + - - +
320D LYS* 6.4 0.4 - - - -
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Residues in contact with GLU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D ASP* 2.8 24.8 + - - +
313D GLU* 1.3 75.3 - - - +
315D THR* 1.3 63.2 + - - +
317D ASN* 3.3 10.3 + - - +
318D LYS* 2.9 52.9 + - + +
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Residues in contact with THR 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D LYS* 3.6 37.3 + - + +
311D PHE* 3.7 30.7 - - + -
312D ASP* 2.7 34.4 + - - -
314D GLU* 1.3 80.6 + - - +
316D LYS* 1.3 57.2 + - - +
318D LYS* 2.9 15.0 + - + +
319D LEU* 2.9 36.0 + - + +
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Residues in contact with LYS 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A HIS* 5.1 7.2 - - - -
305D ILE* 3.7 31.0 - - + +
306D GLU* 2.9 31.9 + - + -
308D MET 3.4 20.4 + - - -
309D GLU* 5.1 0.6 - - - +
311D PHE* 3.3 32.5 + - + -
312D ASP 3.1 17.7 + - - +
313D GLU* 3.9 19.8 + - - +
314D GLU 3.3 0.4 - - - -
315D THR* 1.3 77.1 - - - +
317D ASN* 1.3 58.2 + - - +
319D LEU* 3.4 1.9 + - - +
320D LYS* 3.0 42.8 + - - +
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Residues in contact with ASN 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D LYS* 6.0 1.0 + - - +
313D GLU* 3.0 42.8 + - - +
314D GLU* 3.5 8.1 - - - +
316D LYS* 1.3 76.1 - - - +
318D LYS* 1.3 65.1 + - - +
320D LYS* 4.2 16.5 + - - +
321D ALA* 3.1 22.0 + - - +
322D GLY* 3.2 7.6 + - - -
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Residues in contact with LYS 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D LYS* 4.1 22.7 + - - +
284D ASP* 2.7 35.2 + - - +
314D GLU* 2.9 45.5 + - + +
315D THR* 2.9 12.1 + - - +
317D ASN* 1.3 79.8 - - + +
319D LEU* 1.3 60.9 + - - +
321D ALA 3.7 0.3 + - - -
322D GLY* 3.5 11.5 + - - +
323D ASN* 2.9 46.1 + - - +
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Residues in contact with LEU 319 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274D LEU* 5.1 4.0 - - + -
278D THR* 4.1 11.9 - - + -
283D LYS* 3.9 11.2 - - + +
286D VAL* 3.4 42.2 - - + +
287D ILE* 4.0 1.7 - - - +
288D LEU* 3.1 30.1 + - - +
305D ILE* 3.6 26.5 - - + -
311D PHE* 3.5 40.8 - - + -
315D THR* 2.9 23.6 + - + +
316D LYS 4.0 3.1 - - - +
317D ASN 3.3 0.4 - - - -
318D LYS* 1.3 77.1 - - - +
320D LYS* 1.3 60.1 + - - +
323D ASN* 3.9 7.2 - - - +
324D ALA 6.0 0.2 + - - -
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Residues in contact with LYS 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 3.5 34.2 - - + +
2D LYS* 3.9 27.2 + - + +
3D ILE* 2.8 34.8 + - - +
287D ILE* 6.3 0.7 - - - -
288D LEU* 4.2 5.6 - - + +
302D GLY* 5.2 1.3 - - - +
305D ILE* 4.2 20.4 - - + -
306D GLU* 4.9 17.3 + - + +
313D GLU* 6.4 0.4 - - - -
316D LYS* 3.0 32.1 + - - +
317D ASN* 4.2 16.2 + - - +
318D LYS 3.2 0.2 - - - -
319D LEU* 1.3 79.3 - - - +
321D ALA* 1.3 57.8 + - - +
324D ALA* 5.9 0.7 - - - -
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Residues in contact with ALA 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D LYS* 3.5 26.2 - - + -
3D ILE* 3.8 18.7 - - + +
317D ASN 3.1 5.5 + - - +
318D LYS 3.7 0.4 + - - -
319D LEU 3.6 2.2 + - - -
320D LYS* 1.3 79.3 - - + +
322D GLY* 1.3 64.0 + - - +
323D ASN 3.3 2.2 - - - -
324D ALA* 3.2 7.6 + - - +
325D LEU* 3.0 38.0 + - + +
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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