Contacts of the helix formed by residues 421 - 433 (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 PRO 421 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140D ARG* 3.8 44.6 - - + +
143D ALA* 3.1 13.9 - - + -
144D GLN* 4.2 14.4 - - + +
147D SER* 4.8 5.6 - - - +
419D PRO 4.3 1.6 - - - +
420D HIS* 1.3 104.7 - - + +
422D VAL* 1.3 65.7 + - + +
423D THR 3.4 0.2 - - - -
424D LEU* 5.2 0.2 - - + -
425D ALA* 2.5 40.9 + - + +
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Residues in contact with VAL 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D PHE* 4.3 24.2 - - + +
140D ARG* 4.9 2.9 - - - +
143D ALA* 3.5 13.5 - - + -
420D HIS* 4.1 14.6 - - + +
421D PRO* 1.3 92.7 - - + +
423D THR* 1.3 58.3 + - - +
426D GLY* 2.8 29.5 + - - -
1107D ASP* 5.7 0.2 - - - -
1110D HIS* 3.8 7.1 - - + +
1111D LEU* 3.2 51.1 - - + +
1114D VAL* 4.0 5.4 - - + +
1163D MET* 6.1 1.1 - - - -
1167D LYS* 6.3 0.4 - - - +
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Residues in contact with THR 423 (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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420D HIS* 3.8 14.0 - - - +
421D PRO 3.4 0.2 - - - -
422D VAL* 1.3 77.9 - - - +
424D LEU* 1.3 79.7 + - + +
426D GLY* 3.1 0.7 + - - -
427D MET* 2.8 43.8 + - - +
852D ARG* 5.2 12.8 + - - +
1021D SER* 3.0 26.3 + - - +
1107D ASP* 4.8 7.6 + - - -
1110D HIS* 3.7 24.5 + - + +
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Residues in contact with LEU 424 (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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147D SER* 5.6 2.9 - - - -
150D TYR* 5.4 7.4 - - + -
292D LEU* 4.8 4.5 - - + +
415D LEU* 5.5 12.3 - - + +
416D GLU* 5.0 21.3 - - + -
418D CYS 5.0 4.7 - - - +
420D HIS* 2.7 40.8 - - + +
421D PRO* 5.2 0.2 - - + -
423D THR* 1.3 92.3 - - + +
425D ALA* 1.3 52.1 + - - +
427D MET* 2.7 22.3 - - - +
428D LEU* 2.3 31.8 - - - +
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Residues in contact with ALA 425 (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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143D ALA* 3.3 31.6 - - + +
146D GLN* 4.6 10.5 + - + +
147D SER* 3.6 19.2 - - - +
150D TYR* 6.1 0.4 - - - -
421D PRO 2.5 26.0 + - - +
424D LEU* 1.3 68.0 - - - +
426D GLY* 1.3 57.1 + - - +
428D LEU* 2.8 30.4 - - - +
429D GLU* 4.7 5.0 + - - +
1114D VAL* 5.0 2.4 - - + +
1117D LYS* 4.6 3.6 + - - -
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Residues in contact with GLY 426 (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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422D VAL 2.8 23.7 + - - -
423D THR 3.5 0.4 - - - -
425D ALA* 1.3 79.3 - - - +
427D MET* 1.3 62.2 + - - +
429D GLU* 3.2 19.9 + - - +
430D MET* 3.6 4.0 + - - +
1110D HIS* 3.7 14.8 + - - -
1113D LEU* 5.3 2.4 - - - +
1114D VAL* 4.2 5.6 - - - -
1117D LYS* 3.7 15.4 + - - -
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Residues in contact with MET 427 (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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292D LEU* 3.4 30.1 - - + -
296D SER* 4.8 4.0 - - - +
297D MET* 4.7 8.7 - - + -
415D LEU* 5.1 7.2 - - + -
423D THR* 2.8 35.5 + - - +
424D LEU* 2.7 39.7 - - - +
426D GLY* 1.3 67.2 - - - +
428D LEU* 1.3 53.0 + - + +
429D GLU 2.9 5.2 - - - -
430D MET* 2.7 18.5 + - - +
431D GLY 3.3 0.3 + - - -
846D THR* 2.4 51.0 - - + +
847D ALA* 5.2 10.5 - - + +
1110D HIS* 3.5 13.6 - - + -
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Residues in contact with LEU 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D GLN* 5.4 4.3 - - + +
147D SER* 5.4 1.6 - - - -
150D TYR* 3.3 42.2 - - + -
278D ILE* 4.7 3.3 - - - +
290D ARG* 3.5 28.9 - - + +
291D PHE 4.8 2.0 + - - +
292D LEU* 3.6 24.2 - - + +
424D LEU 2.3 32.8 - - - +
425D ALA* 2.8 29.4 - - + +
427D MET* 1.3 72.6 - - + +
429D GLU* 1.3 58.6 + - - +
431D GLY* 3.6 3.5 + - - -
432D VAL* 3.1 26.2 + - - +
846D THR* 4.6 0.7 - - - -
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Residues in contact with GLU 429 (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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146D GLN* 4.8 6.1 + - - +
290D ARG* 3.6 28.6 + - - +
425D ALA 5.1 3.8 - - - -
426D GLY 3.2 13.1 + - - +
427D MET 2.9 0.4 - - - -
428D LEU* 1.3 80.9 - - - +
430D MET* 1.3 57.1 + - - +
431D GLY 2.8 10.1 + - - -
432D VAL* 2.8 29.6 + - - +
433D SER* 3.3 6.2 + - - -
1113D LEU* 5.1 5.8 - - + +
1117D LYS* 3.3 36.5 - - + +
1128D ARG* 2.7 43.2 + - - +
1129D PHE* 6.0 0.2 - - - -
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Residues in contact with MET 430 (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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426D GLY 3.6 2.9 + - - +
427D MET* 2.7 19.5 + - - +
429D GLU* 1.3 72.5 - - - +
431D GLY* 1.3 57.1 + - - +
433D SER* 4.3 13.5 - - - +
844D VAL* 3.1 38.8 - - + +
845D VAL 5.1 3.1 - - - +
846D THR* 3.8 14.8 - - + -
852D ARG 5.7 1.1 - - - +
853D ARG 4.6 13.5 - - - +
854D ALA* 4.9 1.3 - - - -
860D LEU* 4.3 5.2 - - + -
1109D LEU* 5.6 4.9 - - + -
1110D HIS* 5.2 8.1 - - + -
1113D LEU* 5.4 9.8 - - + +
1130D CYS 5.8 0.2 - - - -
1131D ILE 5.1 0.4 - - - -
1132D SER* 3.3 46.0 - - - +
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Residues in contact with GLY 431 (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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278D ILE* 2.9 37.7 - - - +
279D ARG* 3.8 5.7 + - - -
291D PHE 6.5 0.2 - - - -
427D MET 3.3 6.4 + - - -
428D LEU* 3.9 4.3 - - - -
429D GLU 2.8 0.8 - - - -
430D MET* 1.3 80.7 - - - +
432D VAL* 1.3 59.9 + - - +
433D SER 3.1 2.9 + - - -
844D VAL* 3.7 19.7 + - - +
846D THR* 4.7 4.0 - - - -
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Residues in contact with VAL 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D TYR* 2.7 58.6 - - + +
285D GLN* 4.3 3.1 - - - +
289D MET 4.6 0.4 - - - +
290D ARG* 4.1 10.3 - - + +
428D LEU 3.1 12.7 + - - +
429D GLU* 2.8 27.7 + - - +
431D GLY* 1.3 74.1 - - - +
433D SER* 1.3 72.6 + - - +
434D TYR* 3.3 0.7 + - - +
1128D ARG* 2.8 46.9 - - + +
1129D PHE 4.8 0.2 - - - +
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Residues in contact with SER 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D ARG* 2.3 51.3 + - - -
429D GLU 3.3 5.6 + - - -
430D MET* 4.3 17.3 - - - +
432D VAL* 1.3 88.2 - - - +
434D TYR* 1.3 52.3 + - - +
435D LEU* 4.5 1.4 - - - +
841D LEU* 3.3 1.9 - - - +
844D VAL* 3.6 12.9 - - - +
856D GLU* 4.5 1.9 + - - -
860D LEU* 5.7 1.2 - - - +
1128D ARG* 4.5 0.2 - - - +
1129D PHE 3.4 10.7 + - - -
1130D CYS* 2.4 31.6 + - - +
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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