Contacts of the helix formed by residues 1201 - 1209 (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 SER1201 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447D GLU* 5.0 0.5 + - - -
451D THR* 4.9 15.7 + - - +
797D MET* 6.3 1.7 - - - +
868D ASP* 4.7 3.4 - - - +
869D ARG* 5.2 3.5 - - - -
1198D LYS* 2.3 27.0 - - - +
1199D THR* 3.4 11.1 - - - +
1200D PRO* 1.3 86.5 + - - +
1202D ASN* 1.3 72.4 + - - +
1203D PRO* 3.6 4.3 - - - +
1205D GLY* 3.9 5.5 + - - -
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Residues in contact with ASN1202 (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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447D GLU* 3.6 19.6 + - - +
1200D PRO 2.7 0.4 + - - -
1201D SER* 1.3 89.3 + - - +
1203D PRO* 1.3 59.6 - - - +
1204D THR 3.3 0.4 - - - -
1205D GLY* 2.3 11.9 + - - -
1206D MET* 2.2 42.8 + - + +
256F LEU* 6.1 1.4 - - - +
257F ARG* 4.6 22.2 - - + +
260F LEU* 4.6 20.4 - - - +
261F GLN* 4.9 6.9 - - - +
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Residues in contact with PRO1203 (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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444D TYR* 2.8 8.5 + - + -
447D GLU* 3.2 13.6 - - - +
873D GLU* 2.5 54.5 - - + +
877D MET* 2.8 21.3 - - + -
1197D CYS* 4.2 0.9 - - + +
1200D PRO* 2.4 37.7 - - + +
1201D SER* 3.6 3.4 - - - +
1202D ASN* 1.3 79.5 - - - +
1204D THR* 1.3 50.9 - - - +
1206D MET 2.7 0.9 + - - -
1207D GLU 2.1 34.1 + - - -
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Residues in contact with THR1204 (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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877D MET* 3.5 0.6 - - - +
1196D ASP* 2.9 27.1 - - + +
1197D CYS 1.9 60.4 + - - +
1198D LYS* 2.1 33.6 - - + +
1203D PRO* 1.3 73.8 - - - +
1205D GLY* 1.3 69.6 - - - +
1207D GLU* 2.3 29.0 + - + +
1208D ARG* 2.9 9.3 + - + +
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Residues in contact with GLY1205 (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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1198D LYS* 4.2 14.8 - - - +
1201D SER 3.9 4.5 + - - -
1202D ASN* 2.3 27.0 + - - +
1204D THR* 1.3 82.5 + - - +
1206D MET* 1.3 56.8 + - - -
1208D ARG* 3.6 19.1 + - - +
253F ASP* 3.9 7.3 - - - +
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Residues in contact with MET1206 (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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440D ASN* 4.4 7.6 - - - +
443D ARG* 6.0 6.7 - - + -
444D TYR* 2.5 37.2 - - + +
447D GLU* 4.5 4.0 - - - +
1202D ASN* 2.2 28.0 + - + +
1203D PRO 3.5 0.9 - - - +
1205D GLY 1.3 66.6 - - - -
1207D GLU* 1.3 47.3 - - - -
1209D ARG 2.7 7.3 - - - +
1210D TYR* 2.1 66.8 + - + +
250F GLN* 3.6 18.8 - - - +
253F ASP* 2.9 16.6 + - - +
257F ARG* 2.4 58.1 - - + +
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Residues in contact with GLU1207 (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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876D ALA* 4.9 6.8 - - - +
877D MET* 3.2 17.7 - - + +
1188D CYS* 4.1 13.5 - - - -
1196D ASP* 4.6 8.5 - - + -
1197D CYS* 4.0 15.8 + - - +
1203D PRO 2.1 20.7 + - - +
1204D THR* 2.3 42.6 + - + -
1206D MET 1.3 59.7 - - - -
1208D ARG* 1.3 75.1 + - - +
1209D ARG 2.9 1.6 - - - -
1210D TYR* 2.3 65.4 + - + -
1211D GLY 2.9 0.3 + - - -
1212D ILE* 4.3 8.2 - - - +
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Residues in contact with ARG1208 (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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1196D ASP* 5.8 6.5 - - + -
1198D LYS* 5.2 14.3 - - - +
1204D THR* 2.9 7.3 + - - +
1205D GLY 3.6 16.0 + - - +
1207D GLU* 1.3 84.1 - - - +
1209D ARG* 1.3 79.7 + - - +
1211D GLY* 3.3 21.5 + - - +
1212D ILE 3.5 10.3 - - - +
253F ASP* 5.5 1.0 + - - -
256F LEU* 5.3 3.4 - - - +
277F ASP* 3.1 16.0 + - - +
285F LYS* 2.5 62.4 - - - +
287F ASN* 5.5 0.2 - - - +
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Residues in contact with ARG1209 (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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1206D MET* 2.7 9.7 + - - +
1208D ARG* 1.3 92.9 - - + +
1210D TYR* 1.3 63.6 + - - +
1211D GLY* 3.1 1.6 - - - -
249F ASN* 2.6 51.6 + - + +
250F GLN* 4.4 10.0 + - - +
252F LEU* 2.6 32.8 - - - +
253F ASP* 2.4 61.7 - - - +
256F LEU* 2.7 23.4 - - - +
285F LYS* 2.6 36.5 - - - +
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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