Contacts of the helix formed by residues 316 - 327 (chain C) in PDB entry 3Q41
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 LYS 316 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302C THR* 3.3 13.1 - - + +
314C ILE* 3.9 26.9 + - + +
315C TRP* 1.3 70.0 - - - +
317C THR* 1.3 59.1 + - - +
318C GLY 3.2 0.4 - - - -
319C PRO* 3.4 20.5 - - + +
320C LEU* 4.5 5.0 + - - +
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Residues in contact with THR 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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295C LEU* 3.8 26.0 - - + -
300C ASN 4.6 1.0 + - - -
301C ILE* 3.4 29.1 - - + -
302C THR* 2.7 34.4 + - - +
315C TRP* 2.9 21.2 + - + -
316C LYS* 1.3 76.8 - - - +
318C GLY* 1.3 55.8 + - - +
320C LEU* 3.0 16.3 + - + +
321C PHE* 2.8 33.1 + - + +
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Residues in contact with GLY 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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115C ARG* 3.5 25.1 - - - +
117C PRO* 4.4 1.4 - - - +
315C TRP* 2.7 38.2 + - - -
317C THR* 1.3 70.1 - - - +
319C PRO* 1.4 70.0 - - - +
321C PHE* 3.1 12.8 + - - +
322C LYS* 3.2 10.2 + - - +
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Residues in contact with PRO 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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115C ARG* 3.8 26.7 - - + +
314C ILE* 4.8 6.5 - - + -
315C TRP 3.6 7.0 - - - +
316C LYS* 3.4 24.2 - - + +
318C GLY* 1.4 85.2 - - - +
320C LEU* 1.3 63.6 + - - +
322C LYS* 3.0 19.5 + - + +
323C ARG* 3.3 32.9 + - - +
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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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295C LEU* 3.8 13.9 - - + -
298C LYS* 4.4 18.4 - - + +
299C GLU 5.6 3.1 - - - +
300C ASN 5.5 4.0 - - - +
301C ILE* 5.0 8.7 - - + -
316C LYS 4.5 3.3 + - - +
317C THR* 3.0 26.3 + - + +
319C PRO* 1.3 78.0 - - - +
321C PHE* 1.3 57.9 + - - +
323C ARG* 3.0 30.1 + - + +
324C VAL* 2.9 48.1 + - + +
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Residues in contact with PHE 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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88C TYR* 3.3 34.8 - + + -
89C ALA* 4.1 11.0 - - + -
117C PRO* 3.8 15.3 - - + -
288C VAL* 4.6 8.5 - - + -
291C ALA* 3.4 38.8 - - + -
292C VAL* 3.8 22.9 - - + -
295C LEU* 4.0 24.7 - - + +
315C TRP* 4.5 11.9 - + + -
317C THR 2.8 15.7 + - - +
318C GLY* 3.1 11.9 + - - +
320C LEU* 1.3 73.7 - - - +
322C LYS* 1.3 55.8 + - - +
324C VAL* 3.4 8.1 + - + -
325C LEU* 2.9 32.4 + - + +
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Residues in contact with LYS 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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115C ARG 5.9 0.4 - - - +
117C PRO* 4.2 11.3 - - + +
134C HIS 5.3 0.2 + - - -
135C LEU* 2.8 40.5 + - - +
136C SER* 4.1 15.7 - - - -
137C PHE 4.3 9.6 + - - +
138C LEU* 3.9 21.5 - - + -
318C GLY 3.2 8.4 + - - +
319C PRO* 3.0 13.2 + - + +
321C PHE* 1.3 72.1 - - - +
323C ARG* 1.3 63.6 + - - +
325C LEU* 3.1 8.7 + - - +
326C MET* 2.9 54.9 + - - +
344C GLY* 4.5 12.7 - - - -
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Residues in contact with ARG 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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319C PRO* 3.3 21.0 + - - +
320C LEU* 3.0 41.4 + - + +
322C LYS* 1.3 77.5 - - + +
324C VAL* 1.3 65.8 + - + +
326C MET* 3.3 15.0 + - + +
327C SER* 3.0 29.9 + - - +
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Residues in contact with VAL 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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291C ALA* 3.4 37.2 - - + +
294C GLU* 4.0 22.0 - - + +
295C LEU* 4.2 11.9 - - + +
298C LYS* 4.1 18.2 - - + +
320C LEU* 2.9 38.1 + - + +
321C PHE* 3.4 11.9 - - + +
323C ARG* 1.3 76.6 - - + +
325C LEU* 1.3 52.7 - - - +
327C SER* 3.5 5.6 + - - -
328C SER* 2.7 31.4 + - - +
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Residues in contact with LEU 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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89C ALA* 5.0 2.5 - - + -
117C PRO* 3.8 29.8 - - + -
119C LEU* 4.7 6.3 - - + -
138C LEU* 3.9 20.6 - - + -
287C VAL* 3.4 36.1 - - + +
288C VAL* 4.1 16.8 - - + -
291C ALA* 3.5 13.7 - - + -
321C PHE* 2.9 24.6 + - + +
322C LYS* 3.1 10.5 + - - +
324C VAL* 1.3 77.0 - - - +
326C MET* 1.3 60.5 + - - +
328C SER* 3.2 17.5 + - - -
340C PHE* 3.3 20.2 - - + -
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Residues in contact with MET 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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138C LEU* 4.0 15.5 - - + -
322C LYS* 2.9 49.8 + - - +
323C ARG* 3.3 12.1 + - + +
325C LEU* 1.3 71.9 - - - +
327C SER* 1.3 60.3 + - - +
328C SER 3.2 8.7 + - - +
329C LYS* 4.6 2.9 - - - -
340C PHE* 3.3 34.8 + - + +
341C ASN 3.7 7.9 - - - +
342C GLU* 3.3 32.3 - - + +
344C GLY 3.3 11.2 - - - +
345C ASP* 4.1 12.1 - - + -
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Residues in contact with SER 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C GLU* 5.6 4.5 - - - -
323C ARG* 3.0 17.9 + - - +
324C VAL* 3.9 6.5 - - - -
326C MET* 1.3 75.7 - - - +
328C SER* 1.3 63.6 + - - +
329C LYS* 3.6 21.0 + - - +
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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