Contacts of the helix formed by residues 310 - 316 (chain D) in PDB entry 3S9L
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 310 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78D LYS* 5.0 9.9 - - + -
79D PRO* 4.4 4.8 - - - +
308D ARG* 3.1 19.1 + - - +
309D MET* 1.3 75.9 - - - +
311D ALA* 1.3 57.5 + - - +
312D LYS* 2.8 35.1 + - - +
313D MET* 2.8 20.8 + - - +
314D TYR* 2.9 28.7 + - - +
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Residues in contact with ALA 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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67D VAL* 4.3 16.4 - - + -
71D TYR* 3.7 42.8 - - + -
77D LEU 4.6 0.9 - - - +
78D LYS* 5.1 2.2 - - - +
79D PRO* 4.3 15.2 - - + +
310D ASP* 1.3 74.2 - - - +
312D LYS* 1.3 66.6 + - - +
314D TYR* 3.3 4.8 + - - +
315D LEU* 3.1 30.3 + - + +
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Residues in contact with LYS 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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71D TYR* 5.8 8.4 - - + -
310D ASP* 2.8 15.8 + - - +
311D ALA* 1.3 74.8 - - - +
313D MET* 1.3 51.2 + - - +
316D GLY* 2.6 37.9 + - - -
320D VAL* 3.9 18.2 - - + +
383D ASN* 4.1 28.4 - - + +
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Residues in contact with MET 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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308D ARG* 5.4 6.3 - - + +
309D MET* 3.3 38.8 - - + +
310D ASP* 2.8 30.4 + - - +
312D LYS* 1.3 75.8 - - - +
314D TYR* 1.3 64.8 + - - +
315D LEU 3.4 0.7 + - - -
316D GLY* 3.5 9.9 + - - -
379D ALA* 5.0 10.1 - - + -
382D MET* 3.7 34.3 - - + -
670D LEU* 3.7 30.3 - - + -
673D ALA* 4.6 6.7 - - + -
674D CYS* 4.5 8.1 - - - -
677D ARG* 5.0 3.5 + - - -
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Residues in contact with TYR 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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64D ALA* 5.0 1.8 - - + -
67D VAL* 4.8 6.1 - - + -
79D PRO* 4.0 20.4 - - + -
82D ALA* 3.9 18.5 - - + +
247D PRO* 4.2 12.9 - - + +
248D SER* 2.6 31.0 + - - -
249D HIS 3.9 2.3 + - - -
250D THR* 3.2 40.5 - - + -
305D VAL* 4.5 7.2 - - + -
309D MET* 3.8 22.9 - - - +
310D ASP 2.9 18.3 + - - +
311D ALA* 3.3 6.0 + - - +
313D MET* 1.3 78.4 - - - +
315D LEU* 1.3 73.4 + - + +
677D ARG* 3.2 40.9 + - - -
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Residues in contact with LEU 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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64D ALA* 3.4 35.4 - - + +
67D VAL* 4.4 6.7 - - + -
68D TYR* 4.4 21.1 - - + +
71D TYR* 6.4 0.2 - - + -
247D PRO* 4.3 11.5 - - + +
311D ALA* 3.1 15.1 + - + +
313D MET 4.1 0.2 - - - -
314D TYR* 1.3 93.8 - - + +
316D GLY* 1.3 64.6 + - - +
318D GLU* 5.4 1.2 - - - +
319D TYR* 3.3 42.6 + - + +
320D VAL* 3.7 22.9 - - + -
323D ILE* 4.6 9.9 - - + -
677D ARG* 6.0 0.7 - - - -
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Residues in contact with GLY 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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312D LYS 2.6 24.6 + - - -
313D MET* 3.5 9.6 + - - -
315D LEU* 1.3 73.7 - - - +
317D TYR* 1.3 61.3 + - - -
318D GLU* 3.3 3.1 - - - -
320D VAL* 2.9 31.6 + - - +
382D MET* 6.5 0.9 - - - -
383D ASN* 6.0 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