Contacts of the helix formed by residues 1098 - 1113 (chain P) in PDB entry 1YYL
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 ASN1098 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094P ASN 4.0 9.4 - - - +
1095P MET* 4.0 15.9 + - - +
1096P TRP 3.7 1.4 - - - -
1097P LYS* 1.3 76.8 - - - +
1099P ASN* 1.3 63.9 + - - +
1100P MET* 2.6 56.1 + - - +
1101P VAL* 3.3 26.4 + - + +
1102P GLU* 3.8 8.5 + - - +
1480P ARG* 5.2 1.8 + - - +
1483P LEU 3.7 9.4 + - - +
1486P TYR 2.6 30.7 + - - -
1487P LYS* 4.3 2.4 - - - +
1488P VAL* 5.5 0.3 - - - +
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Residues in contact with ASN1099 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097P LYS 3.8 10.1 + - - -
1098P ASN* 1.3 74.0 + - - +
1100P MET* 1.3 59.4 + - - +
1101P VAL 3.2 0.2 - - - -
1102P GLU* 3.2 13.5 + - + +
1103P GLN* 2.9 28.6 + - - +
1488P VAL* 5.4 10.9 - - + +
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Residues in contact with MET1100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1098P ASN* 2.6 44.1 + - - +
1099P ASN* 1.3 71.6 - - - +
1101P VAL* 1.3 53.1 + - - +
1103P GLN* 3.4 7.7 - - - +
1104P MET* 2.7 37.9 + - - +
1217P TYR* 5.3 9.8 - - + -
1225P ILE* 4.9 10.1 - - - -
1248P THR* 5.0 4.9 - - - -
1483P LEU* 3.7 21.9 - - + +
1486P TYR* 3.1 39.9 - - + -
1487P LYS* 3.1 12.8 - - - +
1488P VAL* 3.4 26.5 - - + +
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Residues in contact with VAL1101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095P MET 4.4 1.3 - - - +
1098P ASN* 3.5 25.6 - - + +
1099P ASN 3.2 0.2 - - - -
1100P MET* 1.3 79.2 - - - +
1102P GLU* 1.3 59.5 + - - +
1105P HIS* 3.0 29.3 + - - +
1476P ARG* 3.4 21.8 - - + +
1479P TRP* 3.7 8.7 - - + -
1480P ARG* 3.0 60.6 - - + +
1483P LEU* 4.0 19.7 - - + -
1484P TYR* 6.3 0.4 - - - -
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Residues in contact with GLU1102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1098P ASN 4.2 7.4 - - - +
1099P ASN* 3.2 19.5 + - + +
1100P MET 3.2 0.2 - - - -
1101P VAL* 1.3 82.9 - - - +
1103P GLN* 1.3 60.8 + - - +
1105P HIS* 3.5 5.5 + - - +
1106P GLU* 3.1 22.5 + - - +
1476P ARG* 2.6 44.6 + - - -
1480P ARG* 4.4 13.9 + - - -
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Residues in contact with GLN1103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099P ASN 2.9 16.6 + - - +
1100P MET* 3.1 9.2 + - - +
1102P GLU* 1.3 75.1 - - - +
1104P MET* 1.3 60.6 + - - +
1106P GLU* 3.1 18.6 + - - +
1107P ASP* 2.9 61.9 + - - +
1217P TYR* 4.1 12.1 - - + -
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Residues in contact with MET1104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100P MET 2.7 20.9 + - - +
1101P VAL 3.9 3.4 - - - +
1103P GLN* 1.3 73.9 - - - +
1105P HIS* 1.3 54.0 + - - +
1107P ASP* 3.0 1.0 + - - +
1108P ILE* 2.7 50.5 + - + +
1215P ILE* 4.8 4.0 - - + -
1217P TYR* 3.0 35.8 + - + +
1251P ILE* 4.5 20.9 - - + -
1253P PRO* 3.8 25.6 - - + -
1479P TRP* 3.7 44.2 - - + +
1482P GLU* 5.8 1.3 - - + -
1483P LEU* 4.1 18.8 - - + -
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Residues in contact with HIS1105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101P VAL 3.0 18.8 + - - +
1102P GLU* 3.6 5.8 - - - +
1104P MET* 1.3 78.4 - - - +
1106P GLU* 1.3 62.4 + - - +
1107P ASP 3.4 0.3 + - - -
1108P ILE* 3.8 1.6 + - - +
1109P ILE* 3.2 45.1 + - + +
1427P TRP* 3.8 16.3 + + - -
1428P GLN 5.3 3.0 + - - -
1474P ASP* 4.5 2.0 + - - -
1475P MET* 3.6 26.5 - - + -
1476P ARG* 3.2 34.9 + - + +
1479P TRP* 2.8 31.1 + - + +
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Residues in contact with GLU1106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102P GLU 3.1 17.2 + - - +
1103P GLN* 3.6 20.4 + - - +
1105P HIS* 1.3 78.4 - - - +
1107P ASP* 1.3 56.3 + - - +
1109P ILE* 3.7 10.0 + - + +
1110P SER* 2.8 41.4 + - - -
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Residues in contact with ASP1107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103P GLN* 2.9 30.9 + - - +
1104P MET 3.3 2.9 - - - +
1106P GLU* 1.3 80.1 - - - +
1108P ILE* 1.3 65.3 + - + +
1109P ILE 2.9 5.0 + - - -
1110P SER* 3.0 7.9 + - - -
1111P LEU* 3.0 31.2 + - + +
1215P ILE* 6.4 0.4 - - + -
1217P TYR* 2.4 44.6 + - - +
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Residues in contact with ILE1108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104P MET* 2.7 42.5 + - + +
1105P HIS 4.4 2.5 - - - +
1107P ASP* 1.3 73.1 - - + +
1109P ILE* 1.3 59.4 + - - +
1111P LEU* 3.7 13.0 - - + +
1112P TRP* 3.0 42.8 + - + +
1215P ILE* 4.0 13.0 - - + -
1253P PRO* 3.5 36.1 - - + -
1255P VAL* 4.8 1.8 - - + -
1427P TRP* 4.0 8.7 - - + -
1479P TRP* 3.8 28.9 - - + -
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Residues in contact with ILE1109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105P HIS* 3.2 41.4 + - + +
1106P GLU* 3.8 11.0 - - + +
1107P ASP 2.9 0.8 - - - -
1108P ILE* 1.3 76.8 - - - +
1110P SER* 1.3 61.4 + - - +
1112P TRP* 3.2 2.6 + - - +
1113P ASP* 2.6 51.1 + - - +
1427P TRP* 3.4 22.9 - - + -
1428P GLN* 3.8 30.7 - - + +
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Residues in contact with SER1110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106P GLU* 2.8 27.4 + - - -
1107P ASP* 3.0 7.9 + - - -
1109P ILE* 1.3 79.3 - - - +
1111P LEU* 1.3 58.3 + - - +
1113P ASP* 3.1 14.8 + - - +
1114P GLN* 2.7 33.2 + - - +
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Residues in contact with LEU1111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107P ASP* 3.0 22.9 + - + +
1108P ILE* 3.7 25.8 - - + +
1110P SER* 1.3 80.2 - - - +
1112P TRP* 1.3 61.8 + - + +
1114P GLN* 3.5 21.7 - - - +
1115P SER* 3.2 27.4 + - - -
1215P ILE* 4.8 18.2 - - + -
1253P PRO* 6.0 0.9 - - + -
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Residues in contact with TRP1112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108P ILE* 3.0 37.4 + - + +
1109P ILE* 3.2 8.6 + - - +
1110P SER 3.1 0.4 - - - -
1111P LEU* 1.3 81.6 - - + +
1113P ASP* 1.3 57.5 + - - +
1114P GLN 2.7 16.9 + - - -
1115P SER* 4.9 0.4 - - - -
1116P LEU* 2.8 67.8 + - + +
1255P VAL* 3.5 25.3 - - + +
1377P ASN* 3.6 32.5 - - + -
1382P PHE* 3.9 21.1 - + - -
1427P TRP* 3.4 27.8 - + + -
1428P GLN* 3.7 14.8 - - - +
1435P TYR* 4.9 1.1 - - - -
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Residues in contact with ASP1113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109P ILE* 2.6 37.8 + - - +
1110P SER* 3.1 8.0 + - - +
1112P TRP* 1.3 73.0 - - - +
1114P GLN* 1.3 59.6 + - - +
1117P LYS* 3.8 26.1 + - - +
1121P LYS* 4.8 11.4 + - - -
1426P MET* 6.0 2.0 - - - +
1428P GLN* 3.9 20.2 + - - +
1429P GLU* 5.5 1.2 - - - +
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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