Contacts of the helix formed by residues 1322 - 1333 (chain C) in PDB entry 7C17
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 SER1322 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1255C THR* 3.6 25.3 - - - -
1296C ASP* 2.5 29.8 + - - -
1321C GLU* 1.3 74.2 - - - +
1323C PHE* 1.3 61.7 + - - +
1324C ASN 3.4 0.9 - - - -
1325C VAL* 3.3 22.0 - - - +
1326C LEU* 3.5 5.4 + - - +
337D ARG* 5.6 1.0 - - - -
341D ASN* 3.5 3.3 + - - +
342D LEU* 3.3 23.8 - - - +
345D LYS* 3.4 14.6 + - - -
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Residues in contact with PHE1323 (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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1296C ASP* 4.1 1.2 + - - -
1319C MET* 4.3 13.7 - - + -
1320C PRO* 3.6 21.6 + - + +
1322C SER* 1.3 75.8 - - - +
1324C ASN* 1.3 60.3 + - - +
1325C VAL 3.2 0.2 - - - -
1326C LEU* 3.2 21.8 + - + +
1327C LEU* 2.9 58.4 + - + +
1337C ILE* 5.9 0.2 - - + -
1339C LEU* 4.5 9.6 - - + -
20D ILE* 3.8 18.8 - - + -
342D LEU* 4.1 8.1 - - + +
1320D ILE* 4.8 6.7 - - + -
1352D ILE* 3.3 41.1 - - + +
1353D VAL* 3.6 36.8 - - + +
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Residues in contact with ASN1324 (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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1319C MET* 3.8 21.0 + - + +
1320C PRO 2.4 28.0 + - - -
1321C GLU* 3.1 43.5 + - - +
1323C PHE* 1.3 76.4 - - - +
1325C VAL* 1.3 65.7 + - - +
1327C LEU* 3.6 15.0 - - + -
1328C LYS* 2.9 41.5 + - + +
99D ARG* 4.4 7.9 + - - +
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Residues in contact with VAL1325 (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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1254C VAL* 4.3 5.6 - - + +
1255C THR* 4.3 12.8 - - + -
1321C GLU 3.4 21.5 - - - +
1322C SER* 3.3 15.4 + - - +
1323C PHE 3.2 0.6 - - - -
1324C ASN* 1.3 79.7 + - - +
1326C LEU* 1.3 57.7 + - - +
1329C GLU* 2.9 33.9 + - - +
99D ARG* 3.4 14.4 - - - +
249D LEU* 3.7 38.0 - - + +
337D ARG* 4.4 24.5 - - - +
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Residues in contact with LEU1326 (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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1322C SER 3.5 1.4 + - - +
1323C PHE* 3.2 22.0 + - + +
1325C VAL* 1.3 81.0 - - + +
1327C LEU* 1.3 57.9 - - + +
1329C GLU* 3.5 8.7 - - - +
1330C ILE* 2.9 51.2 + - + +
331D ILE* 3.8 17.3 - - + -
337D ARG* 4.7 4.7 - - + -
338D PHE* 3.7 43.5 - - + -
342D LEU* 3.8 28.5 - - + -
1320D ILE* 4.4 15.9 - - + -
1352D ILE* 4.8 0.7 - - + -
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Residues in contact with LEU1327 (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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1319C MET* 5.0 5.8 - - + -
1323C PHE* 2.9 52.6 + - + +
1324C ASN* 3.6 17.5 - - + +
1326C LEU* 1.3 77.5 - - + +
1328C LYS* 1.3 60.9 + - + +
1330C ILE* 3.3 8.7 - - + +
1331C ARG* 2.9 43.4 + - - +
1337C ILE* 3.8 37.7 - - + +
1338C GLU* 6.1 2.9 - - - -
1339C LEU* 4.6 16.6 - - + -
20D ILE* 5.7 0.2 - - + -
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Residues in contact with LYS1328 (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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1324C ASN* 2.9 29.1 + - + +
1325C VAL 4.2 2.0 - - - +
1327C LEU* 1.3 72.8 - - - +
1329C GLU* 1.3 52.6 + - - +
1331C ARG* 3.2 38.0 - - - +
1332C SER* 2.7 37.4 + - - -
99D ARG 3.4 18.4 - - - +
100D GLU* 3.8 31.4 + - - +
102D MET* 3.6 20.2 - - + +
245D LEU* 4.5 2.2 - - - -
246D PRO* 3.8 21.7 - - + +
249D LEU* 4.5 2.9 - - + -
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Residues in contact with GLU1329 (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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1325C VAL* 2.9 23.0 + - - +
1326C LEU* 3.5 9.7 - - - +
1327C LEU 3.2 0.4 - - - -
1328C LYS* 1.3 77.2 - - - +
1330C ILE* 1.3 60.2 + - + +
1332C SER* 2.8 18.5 + - - -
1333C LEU* 3.0 17.6 + - + +
245D LEU* 3.8 13.0 - - + +
327D LEU* 3.7 27.1 - - + +
330D MET* 3.4 40.8 - - - +
331D ILE* 3.7 20.3 - - + +
337D ARG* 3.8 20.0 + - - +
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Residues in contact with ILE1330 (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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1326C LEU* 2.9 40.2 + - + +
1327C LEU* 3.3 14.1 - - + +
1329C GLU* 1.3 75.3 - - + +
1331C ARG* 1.3 60.6 + - - +
1333C LEU* 3.7 12.1 - - + +
1334C GLY 3.6 3.1 + - - -
1335C ILE* 3.0 37.7 + - + +
1337C ILE* 3.7 39.3 - - + -
22D ILE* 5.3 6.7 - - + -
331D ILE* 4.6 10.1 - - + -
1319D PHE* 5.9 0.2 - - + -
1320D ILE* 5.8 3.6 - - + -
1332D LEU* 4.1 28.9 - - + -
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Residues in contact with ARG1331 (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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1327C LEU* 2.9 28.3 + - - +
1328C LYS* 3.2 40.9 - - - +
1330C ILE* 1.3 75.8 - - - +
1332C SER* 1.3 63.2 + - - +
1334C GLY* 3.4 9.9 + - - -
1335C ILE 3.5 9.4 + - - +
1336C ASN* 5.0 0.2 + - - -
1337C ILE* 2.9 33.6 + - + +
1338C GLU* 4.0 15.2 + - - +
33D TRP* 3.1 71.6 - - + +
102D MET* 4.2 11.9 - - - +
243D PRO* 3.5 12.1 - - - +
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Residues in contact with SER1332 (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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1328C LYS 2.7 23.2 + - - -
1329C GLU* 2.8 17.0 + - - -
1331C ARG* 1.3 74.6 - - - +
1333C LEU* 1.3 60.5 + - - +
1334C GLY 3.5 0.3 + - - -
102D MET* 4.1 2.8 - - - -
242D LEU* 3.6 12.5 - - - +
243D PRO* 2.9 32.2 - - - +
244D VAL 3.3 31.2 - - - -
245D LEU* 3.7 10.5 - - - +
269D TYR* 3.8 7.9 + - - -
327D LEU* 4.4 3.2 - - - +
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Residues in contact with LEU1333 (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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1329C GLU* 3.0 17.8 + - + +
1330C ILE* 3.7 14.4 - - + +
1331C ARG 3.2 0.8 - - - -
1332C SER* 1.3 78.9 + - - +
1334C GLY* 1.3 50.5 + - - +
1335C ILE* 3.8 15.9 - - + -
113D HIS* 2.4 51.8 + - + -
115D TRP* 3.6 48.5 - - + -
239D LEU* 4.9 0.9 - - - +
242D LEU* 5.1 1.9 - - - +
307D LEU* 3.5 16.2 - - + +
327D LEU* 3.8 34.5 - - + +
331D ILE* 4.8 4.9 - - + -
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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