Contacts of the helix formed by residues 304 - 312 (chain D) in PDB entry 5TJ4
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 LEU 304 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D PHE* 6.0 1.3 - - + -
88D LYS* 3.3 38.1 - - + +
89D LEU* 3.5 12.7 - - + +
108D ILE 4.4 0.6 + - - -
285D LEU* 3.4 39.2 - - + +
286D THR* 3.5 18.6 - - - +
287D ASP* 4.0 4.7 - - - +
290D LEU* 3.5 22.4 - - + -
302D VAL* 3.3 2.5 - - + +
303D ALA* 1.3 76.7 - - - +
305D LYS* 1.3 61.9 + - - +
306D SER* 3.4 19.5 - - - +
307D TYR* 3.3 2.9 + - + +
308D GLU* 2.8 30.4 + - - +
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Residues in contact with LYS 305 (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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87D ASP* 3.1 33.0 + - - +
88D LYS* 3.0 18.3 + - - +
89D LEU 4.0 10.3 + - - -
90D TYR* 3.3 50.9 + - + +
91D PRO* 4.9 7.2 - - - +
303D ALA 3.4 1.2 + - - -
304D LEU* 1.3 70.3 - - - +
306D SER* 1.3 65.6 + - - +
308D GLU* 3.2 1.6 + - - +
309D GLU* 3.1 34.7 + - + +
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Residues in contact with SER 306 (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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88D LYS* 4.6 3.1 + - - +
287D ASP* 3.0 30.1 + - - +
304D LEU* 3.4 18.0 - - - +
305D LYS* 1.3 79.4 - - - +
307D TYR* 1.3 59.4 + - - +
309D GLU* 3.7 20.6 - - - +
310D GLU* 4.1 3.6 + - - +
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Residues in contact with TYR 307 (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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287D ASP* 3.2 34.6 + - + +
290D LEU* 4.0 21.5 - - + -
291D GLU* 3.5 54.1 + - + +
294D ASN* 3.7 19.8 + - + -
295D LYS* 5.7 0.5 - - - +
302D VAL* 4.0 12.3 - - + -
304D LEU* 3.3 6.9 + - + +
306D SER* 1.3 78.2 + - - +
308D GLU* 1.3 64.5 + - - +
309D GLU 3.3 0.2 - - - -
310D GLU* 3.3 18.5 + - + +
311D LEU* 3.2 49.4 + - + +
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Residues in contact with GLU 308 (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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90D TYR* 3.2 35.9 - - + +
301D ALA* 3.4 23.3 - - - +
302D VAL* 3.1 31.6 + - + +
304D LEU 2.8 18.8 + - - +
305D LYS 3.7 0.2 - - - +
307D TYR* 1.3 74.3 - - - +
309D GLU* 1.3 59.3 + - - +
311D LEU* 3.0 9.7 + - - +
312D ALA* 2.8 49.8 + - + +
317D ILE* 4.2 2.6 - - - +
321D MET* 4.1 11.8 - - - +
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Residues in contact with GLU 309 (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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90D TYR* 5.1 4.9 - - - +
305D LYS* 3.1 22.3 + - + +
306D SER* 3.7 14.2 - - - +
307D TYR 3.3 0.2 - - - -
308D GLU* 1.3 77.1 - - - +
310D GLU* 1.3 62.7 + - - +
312D ALA* 3.8 11.8 + - - +
313D LYS* 4.2 4.7 + - - +
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Residues in contact with GLU 310 (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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306D SER 4.1 2.8 + - - +
307D TYR* 3.3 27.1 + - + +
308D GLU 3.2 0.4 - - - -
309D GLU* 1.3 80.7 - - - +
311D LEU* 1.3 62.7 + - + +
312D ALA 3.4 0.2 + - - -
313D LYS* 3.5 17.7 + - - +
314D ASP 4.6 0.5 + - - -
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Residues in contact with LEU 311 (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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294D ASN* 3.6 28.3 - - - +
300D GLY 3.6 23.1 - - - +
302D VAL* 3.6 18.2 - - + -
307D TYR* 3.2 39.7 + - + +
308D GLU* 3.0 17.6 + - - +
310D GLU* 1.3 80.4 - - + +
312D ALA* 1.3 57.6 + - - +
314D ASP* 2.9 32.7 + - + +
317D ILE* 3.5 17.3 - - + +
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Residues in contact with ALA 312 (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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308D GLU* 2.8 36.3 + - + +
309D GLU* 4.0 7.4 - - - +
310D GLU 3.4 0.4 - - - -
311D LEU* 1.3 72.7 - - - +
313D LYS* 1.3 60.7 + - - +
314D ASP 3.4 7.4 + - - +
317D ILE* 4.5 7.4 - - + -
318D ALA* 5.0 7.2 + - - +
321D MET* 5.4 7.2 - - + -
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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