Contacts of the helix formed by residues 1197 - 1210 (chain H) in PDB entry 5TWV
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 GLN1197 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1193H ASP 4.4 4.0 + - - +
1194H ASP 4.0 10.0 + - - +
1195H THR 3.3 2.6 - - - -
1196H THR* 1.3 78.7 - - - +
1198H LEU* 1.3 64.4 + - - +
1200H LEU* 3.2 23.6 + - - +
1201H VAL* 3.8 3.8 + - - +
1234H ASN* 4.2 7.2 - - - +
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Residues in contact with LEU1198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195H THR 4.4 3.7 + - - +
1197H GLN* 1.3 76.9 - - - +
1199H PRO* 1.4 68.1 - - + +
1201H VAL* 3.3 9.3 + - - +
1202H SER* 3.0 19.3 + - - -
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Residues in contact with PRO1199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195H THR 4.2 7.2 - - - +
1196H THR* 3.7 13.7 - - - +
1197H GLN 3.6 3.6 - - - -
1198H LEU* 1.4 91.2 - - + +
1200H LEU* 1.3 54.9 + - - +
1202H SER* 3.3 10.6 - - - -
1203H HIS* 3.0 35.2 + - - +
1230H TYR* 4.8 15.5 - - + -
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Residues in contact with LEU1200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196H THR 4.8 0.6 + - - -
1197H GLN 3.2 13.1 + - - +
1198H LEU 3.2 0.4 - - - -
1199H PRO* 1.3 78.9 - - - +
1201H VAL* 1.3 57.1 + - - +
1203H HIS* 3.3 18.6 + - - +
1204H PHE* 2.9 49.1 + - + -
1230H TYR* 5.2 3.7 - - + -
1231H THR* 6.3 0.2 - - - -
1234H ASN* 3.7 23.8 - - - +
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Residues in contact with VAL1201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422H ALA* 5.8 5.6 - - + -
1197H GLN 3.8 3.4 + - - +
1198H LEU* 3.3 11.7 + - - +
1200H LEU* 1.3 75.8 - - - +
1202H SER* 1.3 60.6 + - - +
1204H PHE* 3.4 16.6 - - + +
1205H ALA* 2.9 28.1 + - - +
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Residues in contact with SER1202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781H ASN* 4.8 18.4 - - - +
1198H LEU 3.0 14.5 + - - -
1199H PRO* 3.2 15.7 + - - -
1201H VAL* 1.3 76.9 - - - +
1203H HIS* 1.3 59.3 + - - +
1205H ALA* 3.2 9.3 + - - +
1206H GLU* 3.0 23.8 + - - +
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Residues in contact with HIS1203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781H ASN* 6.2 0.2 - - - -
1199H PRO 3.0 27.9 + - - -
1200H LEU* 3.3 12.7 - - - +
1202H SER* 1.3 73.0 - - - +
1204H PHE* 1.3 87.7 + + - +
1206H GLU* 3.7 11.7 - - + -
1207H THR* 2.9 26.0 + - - -
1223H PHE* 3.2 31.5 - + + -
1227H LEU* 3.5 14.8 - - + -
1230H TYR* 3.2 51.1 - + + +
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Residues in contact with PHE1204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392H GLN* 5.8 3.6 - - + -
396H TYR* 3.2 53.7 - + + +
418H CYS* 4.8 13.8 - - + +
422H ALA* 4.9 14.8 - - + -
1200H LEU* 2.9 32.7 + - + -
1201H VAL* 3.4 17.9 - - + +
1202H SER 3.1 0.4 - - - -
1203H HIS* 1.3 101.8 - + - +
1205H ALA* 1.3 60.4 + - - +
1207H THR* 3.1 5.7 + - - -
1208H VAL* 2.9 28.4 + - - +
1227H LEU* 3.6 13.0 - - + -
1231H THR* 6.2 4.5 - - - -
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Residues in contact with ALA1205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418H CYS* 6.0 1.3 - - - -
825H GLU* 5.7 9.4 - - + -
1201H VAL 2.9 12.4 + - - +
1202H SER* 3.6 9.9 - - - +
1204H PHE* 1.3 74.6 - - - +
1206H GLU* 1.3 59.2 + - - +
1208H VAL* 3.3 6.5 + - - +
1209H GLU* 2.9 30.2 + - - +
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Residues in contact with GLU1206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780H LEU* 4.8 10.5 - - + +
781H ASN* 4.5 21.1 - - + +
1202H SER 3.0 15.4 + - - +
1203H HIS* 3.8 12.8 - - + -
1205H ALA* 1.3 77.0 - - - +
1207H THR* 1.3 61.2 + - - +
1209H GLU* 4.0 5.6 - - - +
1210H GLY* 3.1 22.3 + - - -
1223H PHE* 5.6 2.2 - - + -
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Residues in contact with THR1207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396H TYR* 4.8 13.2 - - - -
1203H HIS 2.9 20.2 + - - -
1204H PHE* 3.1 9.6 + - - -
1206H GLU* 1.3 78.6 - - - +
1208H VAL* 1.3 60.2 + - - +
1210H GLY 4.4 1.3 - - - +
1211H LEU* 4.2 16.1 + - - +
1223H PHE* 3.7 25.6 - - - -
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Residues in contact with VAL1208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414H ALA* 5.0 5.6 - - + +
415H GLY* 4.7 15.0 - - - +
418H CYS* 4.7 16.6 - - + -
1204H PHE 2.9 14.8 + - - +
1205H ALA* 3.9 6.3 - - - +
1206H GLU 3.3 0.2 - - - -
1207H THR* 1.3 77.1 - - - +
1209H GLU* 1.3 65.4 + - - +
1211H LEU* 4.1 10.9 + - - +
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Residues in contact with GLU1209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778H TRP* 5.0 18.2 - - + +
779H LEU 5.0 10.8 - - - +
1205H ALA 2.9 17.8 + - - +
1206H GLU* 4.0 6.5 - - - +
1207H THR 3.3 0.2 - - - -
1208H VAL* 1.3 79.4 - - - +
1210H GLY* 1.3 58.2 + - - +
1211H LEU* 3.1 7.5 + - - +
1212H THR 4.8 0.9 + - - -
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Residues in contact with GLY1210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778H TRP* 5.8 3.6 - - - -
1206H GLU 3.1 12.4 + - - -
1207H THR* 4.4 4.2 - - - +
1208H VAL 3.7 0.2 - - - -
1209H GLU* 1.3 77.4 - - - +
1211H LEU* 1.3 52.5 + - - +
1212H THR 3.4 1.8 - - - -
1213H THR* 3.2 19.2 + - - -
1214H ILE* 2.7 31.9 + - - +
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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