Contacts of the strand formed by residues 1127 - 1133 (chain D) in PDB entry 3IKM
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 GLY1127 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285D GLN* 5.1 1.7 - - - +
1120D PHE* 4.6 9.7 - - - -
1125D ILE* 4.6 10.5 - - - +
1126D ASP* 1.3 80.1 + - - +
1128D ARG* 1.3 68.2 + - - +
1140D LEU* 3.6 14.5 + - - -
1141D VAL* 4.9 0.2 - - - -
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Residues in contact with ARG1128 (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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285D GLN* 2.6 37.0 - - - +
288D ARG* 5.5 8.3 - - - +
290D ARG* 6.1 2.0 - - - +
429D GLU* 2.7 62.9 + - - +
432D VAL* 2.8 27.0 - - + +
433D SER 4.5 1.2 - - - +
434D TYR* 6.4 0.2 - - - -
1117D LYS* 4.1 8.5 - - - +
1120D PHE* 5.6 2.7 - - - -
1127D GLY* 1.3 77.0 - - - +
1129D PHE* 1.3 122.6 + - - +
1140D LEU* 2.7 36.4 + - + +
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Residues in contact with PHE1129 (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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285D GLN* 4.6 0.4 - - - +
429D GLU 6.0 0.4 - - - -
432D VAL 4.6 0.2 - - - -
433D SER* 3.4 9.9 + - - -
434D TYR* 3.1 21.5 + - - +
1113D LEU* 3.8 33.7 - - + -
1116D MET* 4.9 4.5 - - + -
1117D LYS* 4.7 6.1 - - + -
1120D PHE* 5.8 2.9 - + - -
1128D ARG* 1.3 131.4 + - - +
1130D CYS* 1.3 67.1 + - - +
1131D ILE* 4.6 9.0 - - + -
1137D VAL* 4.5 4.7 - - + -
1138D ARG 3.0 20.4 - - - +
1139D TYR* 3.0 54.7 - + - -
1140D LEU* 3.5 2.5 - - - +
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Residues in contact with CYS1130 (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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430D MET* 5.8 0.4 - - - -
433D SER* 2.4 26.7 + - - -
434D TYR* 2.6 43.1 - - - +
435D LEU* 3.9 13.5 - - + +
436D PRO* 5.1 5.2 - - - -
860D LEU* 5.4 2.3 - - - +
886D LEU* 5.2 10.5 - - - -
1129D PHE* 1.3 83.1 - - - +
1131D ILE* 1.3 69.3 + - + +
1138D ARG* 3.7 16.2 - - - -
1139D TYR 5.4 0.2 - - - -
1140D LEU* 4.8 10.8 - - - -
1189D LEU* 6.0 2.5 - - - -
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Residues in contact with ILE1131 (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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430D MET* 5.1 0.9 - - - -
435D LEU* 4.6 15.0 - - + -
859D TRP 5.9 0.2 - - - +
860D LEU* 5.1 0.7 - - + -
1129D PHE* 4.3 7.3 - - + -
1130D CYS* 1.3 86.0 - - + +
1132D SER* 1.3 52.7 + - - +
1133D ILE* 3.5 21.1 - - + -
1136D GLU* 2.3 24.1 - - + +
1137D VAL* 2.8 9.7 - - - +
1138D ARG* 2.3 76.1 - - + +
1189D LEU* 5.7 6.7 - - + -
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Residues in contact with SER1132 (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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430D MET* 3.3 39.0 - - - +
853D ARG 4.6 2.9 + - - -
854D ALA* 4.5 5.7 - - - +
860D LEU* 2.8 25.4 - - - +
1109D LEU* 3.9 25.4 - - - +
1113D LEU* 5.7 2.5 - - - -
1131D ILE* 1.3 68.3 - - - +
1133D ILE* 1.3 66.6 + - - +
1134D HIS 4.0 0.5 + - - -
1136D GLU 2.6 9.9 - - - -
1137D VAL* 4.8 0.2 - - - -
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Residues in contact with ILE1133 (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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859D TRP 4.0 13.2 - - - +
860D LEU* 3.2 32.3 - - + +
862D ALA* 4.6 16.6 - - + +
875D LYS* 6.2 3.4 - - + +
1109D LEU* 6.0 1.0 - - - +
1131D ILE* 3.5 25.6 - - + -
1132D SER* 1.3 86.2 + - - +
1134D HIS* 1.3 83.1 - - + +
1135D ASP 2.2 23.2 + - - -
1136D GLU* 2.3 45.7 + - + +
1138D ARG* 5.7 0.2 - - - +
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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