Contacts of the helix formed by residues 278 - 289 (chain C) in PDB entry 3DC1
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 278 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C PRO* 3.8 40.8 - - + +
107C GLY 4.2 0.2 - - - -
108C GLN* 3.0 25.6 + - + +
110C ASP* 3.3 37.5 - - + +
276C GLY 3.6 0.4 + - - -
277C PRO* 1.3 68.3 - - - +
279C PRO* 1.4 72.6 - - + +
281C ILE* 3.1 2.4 + - - +
282C GLU* 2.9 41.9 + - + +
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Residues in contact with PRO 279 (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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3C TYR* 3.9 33.9 - - + -
7C ILE* 4.7 4.8 - - + +
104C PRO 3.7 15.9 - - - +
105C SER* 4.1 10.1 - - - +
107C GLY* 4.2 1.6 - - - -
277C PRO* 3.2 13.9 - - + +
278C LYS* 1.4 97.7 - - + +
280C LEU* 1.3 58.9 + - - +
282C GLU* 3.5 11.0 - - + +
283C ARG* 3.3 28.4 - - - +
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Residues in contact with LEU 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C TYR* 3.6 42.8 - - + +
6C PHE* 4.8 9.4 - - + +
7C ILE* 4.0 27.1 - - + -
127C MET* 3.7 29.3 - - + +
226C LEU* 4.3 14.1 - - + -
256C ILE* 3.7 28.5 - - + -
277C PRO* 2.8 23.2 + - + +
279C PRO* 1.3 75.0 - - - +
281C ILE* 1.3 66.7 + - + +
282C GLU 3.2 1.1 - - - -
283C ARG 3.3 8.8 + - - -
284C VAL* 3.5 9.8 + - - +
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Residues in contact with ILE 281 (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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110C ASP* 3.7 20.9 - - + +
112C CYS* 3.5 32.5 - - + +
124C VAL* 6.2 0.2 - - + -
256C ILE* 5.1 4.3 - - + -
274C LEU* 4.1 24.5 - - + +
275C THR 4.3 2.0 - - - -
276C GLY* 3.3 46.2 - - - +
277C PRO 3.1 4.4 + - - +
278C LYS 3.1 4.9 + - - +
280C LEU* 1.3 74.8 - - + +
282C GLU* 1.3 67.7 + - - +
284C VAL* 3.1 7.5 + - + +
285C ILE* 2.8 39.0 + - + +
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Residues in contact with GLU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ASP* 5.0 1.3 + - - +
278C LYS* 2.9 33.4 + - + +
279C PRO* 3.5 13.1 - - - +
281C ILE* 1.3 77.0 - - - +
283C ARG* 1.3 74.9 + - - +
285C ILE* 2.8 32.9 + - + +
286C LEU* 2.8 33.0 + - + +
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Residues in contact with ARG 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 4.3 16.2 - - + -
11C SER* 3.0 39.4 + - - +
12C ALA* 3.4 12.6 + - - +
14C ARG* 2.7 42.0 + - - +
127C MET* 3.4 32.1 - - + -
279C PRO 3.3 20.4 - - - +
281C ILE 3.3 0.8 - - - -
282C GLU* 1.3 93.2 + - - +
284C VAL* 1.3 58.2 + - - +
286C LEU* 3.7 15.6 - - - +
287C HIS* 3.1 26.7 + - - +
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Residues in contact with VAL 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C CYS* 4.8 5.6 - - - -
114C THR* 5.1 0.2 - - + -
120C GLY* 4.8 6.3 - - - -
123C LYS* 3.8 31.4 - - + +
124C VAL* 4.1 25.6 - - + -
127C MET* 4.5 4.7 - - + -
274C LEU* 4.2 18.2 - - + -
280C LEU 3.7 13.2 - - - +
281C ILE* 3.1 8.2 + - - +
283C ARG* 1.3 75.6 - - - +
285C ILE* 1.3 54.3 + - + +
287C HIS* 3.0 7.6 + - - +
288C ILE* 2.7 52.5 + - + +
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Residues in contact with ILE 285 (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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77C SER* 4.1 22.2 - - - -
78C ALA* 3.7 24.5 - - + +
110C ASP* 4.8 6.7 - - - +
111C LEU 5.2 1.8 - - - +
112C CYS* 4.1 12.8 - - + -
281C ILE* 2.8 40.2 + - + +
282C GLU* 2.8 20.7 + - + +
284C VAL* 1.3 70.2 - - - +
286C LEU* 1.3 60.4 + - + +
288C ILE* 3.1 12.6 + - + +
289C GLN* 3.0 36.6 + - - +
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Residues in contact with LEU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ARG* 3.5 43.2 - - + +
15C ASN 4.5 6.7 - - - +
16C PRO* 3.8 26.5 - - + -
282C GLU* 2.8 35.8 + - + +
283C ARG* 3.6 24.7 - - - +
285C ILE* 1.3 79.9 - - + +
287C HIS* 1.3 62.5 + - - +
289C GLN* 3.4 38.8 + - - +
290C VAL* 3.8 12.0 + - - +
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Residues in contact with HIS 287 (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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14C ARG* 3.2 39.1 + - - +
123C LYS* 3.2 36.2 + - + +
126C GLU* 2.8 34.2 + - + +
283C ARG 3.1 14.7 + - - +
284C VAL* 3.0 11.6 + - - +
286C LEU* 1.3 75.7 - - - +
288C ILE* 1.3 62.1 + - - +
290C VAL* 3.4 13.6 + - + +
291C SER* 3.1 13.0 + - - -
122D CYS* 4.6 3.7 - - - -
126D GLU* 2.9 27.0 + - - -
287D HIS* 6.1 0.2 - - - -
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Residues in contact with ILE 288 (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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77C SER 4.0 13.5 - - - +
78C ALA* 6.3 0.2 - - - -
112C CYS* 5.2 4.3 - - + -
113C VAL 4.7 8.1 - - - +
114C THR* 4.2 14.4 - - + -
119C GLN* 4.1 20.9 - - + +
123C LYS* 3.9 19.1 - - + -
284C VAL* 2.7 37.5 + - + +
285C ILE* 3.1 13.4 + - - +
287C HIS* 1.3 70.8 - - - +
289C GLN* 1.4 51.5 + - - +
290C VAL 2.9 10.0 + - - -
291C SER* 2.9 9.6 + - - -
292C THR* 3.2 7.7 + - - +
293C LEU 2.8 56.2 + - - +
294C HIS* 4.2 2.5 - - - +
295C PRO* 5.9 0.2 - - + -
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Residues in contact with GLN 289 (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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16C PRO* 3.6 7.3 - - - +
17C SER* 2.7 55.2 + - - +
18C PRO* 4.1 13.3 - - - +
77C SER* 2.7 34.8 + - - +
285C ILE* 3.0 20.7 + - - +
286C LEU* 3.5 21.5 - - - +
287C HIS 3.3 0.6 - - - -
288C ILE* 1.4 72.8 - - - +
290C VAL* 1.3 61.7 + - - +
293C LEU* 3.1 27.8 - - - +
118D GLN* 5.3 0.9 + - - -
142D TYR* 5.5 0.7 + - - -
144D GLY* 5.5 2.3 - - - -
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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