Contacts of the strand formed by residues 1217 - 1222 (chain C) in PDB entry 1I7M
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 VAL1217 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215C GLY 5.7 0.7 - - - +
1216C SER* 1.3 71.4 - - - +
1218C ILE* 1.3 64.7 + - - +
1219C ASP 4.2 0.2 + - - -
1231C ASN 4.0 0.9 - - - +
1232C GLY* 3.6 2.8 - - - -
1233C MSE 3.0 39.0 + - + +
1055D THR* 4.1 24.8 - - + +
1056D LYS 5.8 0.4 - - - +
1057D THR* 5.0 14.8 - - + -
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Residues in contact with ILE1218 (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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1204C THR* 4.1 11.9 - - + -
1210C ARG* 4.1 31.6 - - + +
1216C SER* 3.4 17.5 + - - +
1217C VAL* 1.3 82.4 - - - +
1219C ASP* 1.3 70.5 + - - +
1220C ALA* 4.1 9.8 + - + +
1230C MSE 3.9 26.2 - - + -
1231C ASN 3.5 8.3 - - - +
1240C TRP* 4.0 24.0 - - + -
1055D THR* 5.7 0.4 - - - -
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Residues in contact with ASP1219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1217C VAL 4.2 0.4 + - - -
1218C ILE* 1.3 74.8 - - - +
1220C ALA* 1.3 68.5 + - - +
1221C THR* 4.6 1.2 + - - -
1230C MSE 3.5 1.4 - - - -
1231C ASN* 3.0 34.7 + - + +
1053D SER* 2.6 35.7 + - - -
1054D VAL* 4.1 3.9 + - - -
1055D THR* 3.2 31.7 + - + +
1062D ALA 4.9 1.7 - - - +
1064D VAL* 3.7 13.5 + - + +
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Residues in contact with ALA1220 (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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1200C ALA* 3.5 19.2 - - + +
1201C LYS* 5.3 0.9 - - - +
1204C THR* 3.4 24.9 - - - +
1218C ILE* 4.0 8.4 + - + +
1219C ASP* 1.3 80.2 + - - +
1221C THR* 1.3 65.5 + - - +
1228C TYR* 3.6 17.0 - - + +
1229C SER 3.4 7.4 - - - +
1230C MSE 4.2 3.4 - - + -
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Residues in contact with THR1221 (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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1200C ALA* 4.2 4.9 - - - -
1219C ASP* 4.6 1.4 + - - -
1220C ALA* 1.3 75.6 + - - +
1222C MSE 1.3 75.9 + - - +
1223C PHE* 4.1 16.1 + - + -
1228C TYR* 3.4 6.9 - - - -
1229C SER 2.9 35.5 + - - +
1052D ILE* 3.6 33.2 - - + +
1053D SER* 4.3 6.2 + - - -
1064D VAL* 4.1 18.8 - - - +
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Residues in contact with MSE1222 (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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1191C GLN 3.1 28.9 - - - +
1192C PHE* 3.5 3.1 - - - -
1193C TYR 3.4 27.4 - - - +
1194C MSE 4.0 31.7 - - + +
1195C LYS 5.4 0.4 - - - +
1198C VAL* 5.7 5.6 - - + +
1199C THR 5.7 0.2 - - - -
1200C ALA* 4.1 16.6 - - + +
1203C VAL* 3.5 22.7 - - + -
1221C THR* 1.3 84.8 - - - +
1223C PHE* 1.3 65.4 + - - +
1224C ASN 4.2 0.3 + - - -
1227C GLY 3.6 8.7 - - - +
1228C TYR* 3.7 27.6 - - - -
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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