Contacts of the helix formed by residues 315 - 327 (chain C) in PDB entry 1T9D
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 315 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313C HIS* 2.8 30.6 + - + -
314C ALA* 1.3 75.6 - - - +
316C GLY* 1.3 65.4 + - - +
317C PRO* 3.6 1.3 - - - -
318C ARG* 3.4 48.0 + - - +
319C LEU* 3.2 18.5 + - + +
428C THR* 3.3 15.1 - - + +
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Residues in contact with GLY 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C ILE* 3.3 25.3 - - - +
313C HIS 2.9 9.3 + - - -
314C ALA 3.0 2.0 - - - -
315C ASP* 1.3 79.4 - - - +
317C PRO* 1.3 67.9 - - - +
319C LEU* 4.1 1.0 - - - +
320C LEU* 3.0 20.1 + - - +
428C THR* 3.2 21.5 - - - +
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Residues in contact with PRO 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C ILE* 4.1 5.3 - - - +
311C LEU* 4.3 9.4 - - + -
313C HIS 4.1 4.3 - - - +
314C ALA 3.8 10.5 - - - +
316C GLY* 1.3 87.9 - - - +
318C ARG* 1.3 63.6 + - - +
320C LEU* 3.1 7.4 + - + +
321C LYS* 2.8 25.7 + - - +
340C SER* 3.5 26.1 - - - +
513C PRO* 4.0 35.0 - - + -
514C HIS* 5.9 2.2 - - - +
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Residues in contact with ARG 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C ALA 5.5 0.2 - - - +
315C ASP* 3.4 47.7 + - - +
316C GLY 3.2 1.0 - - - -
317C PRO* 1.3 83.3 - - - +
319C LEU* 1.3 82.6 + - - +
321C LYS* 3.0 4.9 + - - +
322C GLU* 3.0 46.9 + - + +
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Residues in contact with LEU 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C ASP* 3.2 11.8 + - + +
316C GLY 4.2 1.6 - - - +
318C ARG* 1.3 101.8 - - - +
320C LEU* 1.3 61.8 + - - +
322C GLU* 3.7 24.0 - - - +
323C LEU* 3.1 7.1 + - - +
428C THR* 3.0 44.0 - - + +
431C LEU* 4.5 11.8 - - + +
432C GLY* 3.8 22.7 - - - +
435C MET* 3.1 31.9 - - + +
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Residues in contact with LEU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C LEU* 3.7 17.4 - - + +
306C VAL* 3.6 45.5 - - + -
310C ILE* 4.0 14.6 - - + -
316C GLY 3.0 13.8 + - - +
317C PRO* 3.2 8.7 - - + +
318C ARG 3.0 1.0 + - - -
319C LEU* 1.3 77.8 - - - +
321C LYS* 1.3 63.6 + - - +
323C LEU* 3.2 12.7 + - + +
324C SER* 3.3 11.8 + - - -
331C VAL* 4.9 0.4 - - + -
340C SER* 3.9 26.9 - - - +
341C PHE* 4.6 14.4 - - + -
373C VAL* 5.4 3.1 - - + -
431C LEU* 4.3 16.5 - - + +
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Residues in contact with LYS 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C PRO 2.8 18.4 + - - +
318C ARG* 3.6 4.7 - - - +
320C LEU* 1.3 73.7 - - - +
322C GLU* 1.3 62.1 + - + +
324C SER* 3.1 16.1 + - - -
325C ASP* 3.1 33.7 + - - +
341C PHE* 4.6 19.0 - - + -
342C ASP* 4.8 13.8 - - + +
345C ASP* 3.6 28.5 + - - +
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Residues in contact with GLU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C ARG* 3.0 52.5 + - + +
319C LEU* 3.6 17.6 - - - +
320C LEU 3.2 0.2 - - - -
321C LYS* 1.3 77.9 - - + +
323C LEU* 1.3 60.1 + - - +
325C ASP* 3.5 11.6 + - - +
326C ARG* 3.5 27.8 + - - +
435C MET* 3.6 20.7 - - + +
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Residues in contact with LEU 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C ILE* 5.4 7.6 - - + -
304C LEU* 4.4 28.0 - - + -
319C LEU 3.1 13.1 + - - +
320C LEU 3.6 8.1 - - - +
321C LYS 3.2 0.2 - - - -
322C GLU* 1.3 74.3 - - - +
324C SER* 1.3 64.6 + - - +
326C ARG* 5.3 0.7 - - + -
327C ALA* 3.5 28.3 + - + +
329C ILE* 4.8 5.3 - - + +
371C ILE* 5.0 7.0 - - + -
373C VAL* 5.7 0.7 - - + -
431C LEU* 3.6 34.1 - - + +
434C MET* 5.5 4.0 - - + -
435C MET* 3.4 24.9 - - + +
438C ILE* 4.2 24.0 - - + -
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Residues in contact with SER 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C LEU* 4.5 4.2 - - - +
320C LEU 3.3 6.5 + - - -
321C LYS 3.1 9.5 + - - -
323C LEU* 1.3 78.2 - - - +
325C ASP* 1.3 62.4 + - - +
328C GLN* 3.0 26.9 - - - -
329C ILE* 2.7 29.9 + - - +
331C VAL* 3.5 20.8 - - - +
341C PHE* 4.2 8.2 - - - -
347C LYS* 3.2 21.1 + - - +
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Residues in contact with ASP 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C LYS* 3.1 37.8 + - - +
322C GLU* 3.7 12.0 - - - +
323C LEU 3.2 0.2 - - - -
324C SER* 1.3 80.3 - - - +
326C ARG* 1.3 69.2 + - + +
328C GLN* 3.0 26.0 + - - +
345C ASP* 4.9 1.7 - - - +
347C LYS* 4.4 11.1 + - - -
441C VAL 4.6 1.9 - - - +
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Residues in contact with ARG 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C GLU* 3.5 14.0 + - - +
323C LEU* 4.5 2.0 - - - +
325C ASP* 1.3 79.9 - - + +
327C ALA* 1.3 60.9 + - - +
328C GLN 3.0 4.3 + - - -
435C MET* 2.7 52.2 + - - +
436C SER* 4.0 11.3 + - - +
438C ILE* 2.6 37.3 + - + +
440C PRO* 4.1 28.5 - - + +
441C VAL* 2.9 29.5 + - - +
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Residues in contact with ALA 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C ILE* 4.5 9.0 - - + -
323C LEU* 3.5 13.3 + - + +
326C ARG* 1.3 78.3 - - - +
328C GLN* 1.3 66.3 + - - +
329C ILE* 3.5 28.6 + - + +
438C ILE* 3.9 20.4 - - + +
439C PHE 4.4 0.7 - - - +
441C VAL* 3.7 14.8 - - + +
444C ARG* 2.9 19.4 + - - -
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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