Contacts of the helix formed by residues 1234 - 1246 (chain D) in PDB entry 2NQB
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 TYR1234 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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825C PHE* 4.2 14.8 - + + -
826C PRO* 4.2 16.8 - - + -
829C ARG* 4.8 8.3 - - + -
830C ILE* 4.0 10.3 - - + +
833C LEU* 3.3 28.6 - - + +
855C MET* 3.6 24.1 - - + +
1233D SER* 1.3 74.8 - - - +
1235D ALA* 1.3 58.8 + - - +
1236D ILE 3.4 2.2 - - - -
1237D TYR* 3.0 24.5 + + + -
1238D ILE* 2.8 43.0 + - + +
1260D ASN* 2.8 21.6 + - - +
1263D VAL* 3.7 22.9 - - + -
1264D ASN* 3.3 28.6 + - - -
1267D PHE* 4.7 4.3 - - - -
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Residues in contact with ALA1235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233D SER* 3.1 17.8 + - - +
1234D TYR* 1.3 75.8 - - - +
1236D ILE* 1.3 59.8 + - + +
1238D ILE* 3.2 1.0 + - - -
1239D TYR* 2.8 26.9 + - - +
1256D MET* 3.2 41.5 - - + +
1260D ASN* 4.0 4.3 + - + +
268J G 6.2 0.2 - - - +
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Residues in contact with ILE1236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233D SER 4.8 0.6 + - - +
1235D ALA* 1.3 78.3 - - + +
1237D TYR* 1.3 85.5 + - + +
1239D TYR* 3.5 7.4 + - - +
1240D THR* 3.0 30.7 + - - -
267J G 3.7 35.9 - - + +
268J G 3.7 24.0 + - - +
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Residues in contact with TYR1237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824C GLN* 3.1 26.4 - - + +
825C PHE* 3.8 24.5 - - + -
826C PRO* 3.6 37.8 - - + +
829C ARG* 3.5 26.2 + - - -
1233D SER 4.0 0.2 - - - -
1234D TYR* 3.0 20.8 + + - +
1236D ILE* 1.3 97.3 - - + +
1238D ILE* 1.3 67.2 + - - +
1240D THR* 3.3 6.9 + - - -
1241D VAL* 3.1 27.9 + - - +
267J G 3.2 38.4 + - - -
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Residues in contact with ILE1238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825C PHE* 4.2 15.7 - - + -
859C ALA* 5.2 1.1 - - + -
863C LEU* 3.7 21.9 - - + +
1234D TYR* 2.8 35.4 + - + +
1235D ALA 3.6 5.6 - - - +
1237D TYR* 1.3 77.6 - - - +
1239D TYR* 1.3 56.0 + - - +
1241D VAL* 3.2 4.6 + - - -
1242D LEU* 2.9 28.7 + - + +
1251D ILE* 5.0 1.3 - - + -
1256D MET* 3.6 24.0 - - + -
1259D MET* 3.8 27.4 - - + +
1260D ASN* 3.7 31.9 - - - +
1263D VAL* 4.1 5.8 - - + -
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Residues in contact with TYR1239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1235D ALA 2.8 16.8 + - - +
1236D ILE* 3.6 8.5 - - - +
1238D ILE* 1.3 78.1 - - - +
1240D THR* 1.3 64.9 + - - +
1242D LEU* 3.2 12.3 + - + +
1243D LYS* 3.0 64.6 + - + +
1250D GLY* 5.1 0.2 - - - -
1251D ILE* 4.1 22.0 - - + -
1256D MET* 3.9 8.0 - - + +
20I T 3.8 50.7 + - + -
21I T 4.5 10.1 + - - -
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Residues in contact with THR1240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824C GLN* 3.5 35.1 + - + +
1236D ILE 3.0 15.9 + - - -
1237D TYR* 3.7 9.5 - - - -
1238D ILE 3.3 0.4 - - - -
1239D TYR* 1.3 78.3 - - - +
1241D VAL* 1.3 64.2 + - - +
1243D LYS* 3.2 9.9 + - + +
1244D GLN* 3.1 27.3 + - + +
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Residues in contact with VAL1241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824C GLN* 4.3 12.3 - - + -
825C PHE* 3.9 18.8 - - + -
856C GLU* 3.9 16.8 - - + +
859C ALA* 4.7 1.1 - - + -
860C ALA* 3.7 40.6 - - + +
863C LEU* 4.2 7.0 - - + -
1237D TYR 3.1 15.6 + - - +
1238D ILE* 3.7 7.2 - - - +
1240D THR* 1.3 75.7 - - - +
1242D LEU* 1.3 64.2 + - - +
1244D GLN* 3.1 26.8 + - - +
1245D VAL* 3.2 13.9 + - + +
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Residues in contact with LEU1242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863C LEU* 3.8 21.5 - - + +
878C ILE* 3.8 23.8 - - + -
1238D ILE* 2.9 15.7 + - + +
1239D TYR* 3.4 18.4 - - + +
1241D VAL* 1.3 76.4 - - - +
1243D LYS* 1.3 54.0 + - + +
1245D VAL* 3.1 11.0 + - + +
1246D HIS* 2.7 49.1 + - + +
1249D THR* 3.6 24.2 - - - +
1250D GLY* 3.8 19.5 - - - +
1251D ILE* 4.0 20.2 - - + -
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Residues in contact with LYS1243 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1239D TYR* 3.0 57.8 + - + +
1240D THR* 3.2 10.5 + - + +
1242D LEU* 1.3 77.2 - - + +
1244D GLN* 1.3 60.4 + - + +
1245D VAL 3.4 0.2 - - - -
1246D HIS 3.9 4.9 - - - +
1247D PRO* 3.3 49.9 + - + +
1248D ASP* 4.3 1.6 - - - +
1249D THR 2.7 31.6 + - - +
1250D GLY* 4.5 1.0 - - - -
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Residues in contact with GLN1244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824C GLN* 4.1 32.2 - - - +
856C GLU* 5.0 4.2 - - - +
1240D THR* 3.1 19.7 + - + +
1241D VAL* 3.1 21.4 + - - +
1243D LYS* 1.3 79.3 - - - +
1245D VAL* 1.3 62.9 + - + +
1247D PRO* 4.7 5.4 - - - +
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Residues in contact with VAL1245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860C ALA* 4.3 24.7 - - + +
863C LEU* 4.2 16.4 - - + -
864C GLU* 3.1 27.5 - - + +
1241D VAL* 3.6 13.0 - - + +
1242D LEU* 3.2 15.9 - - + +
1244D GLN* 1.3 82.2 - - + +
1246D HIS* 1.3 89.0 + - + +
1247D PRO* 3.8 6.1 - - - +
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Residues in contact with HIS1246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863C LEU 3.5 20.4 - - - -
864C GLU* 3.0 32.2 + - - -
867C GLY* 3.5 16.0 - - - -
868C ASN* 3.2 23.3 + - - -
871C ARG* 4.1 21.9 + - - +
1242D LEU* 2.7 24.4 + - + +
1243D LYS* 3.9 2.8 - - - -
1245D VAL* 1.3 91.5 + - + +
1247D PRO* 1.3 67.5 - - - +
1248D ASP 3.1 3.5 + - - -
1249D THR* 3.1 36.6 + - - +
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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