Contacts of the helix formed by residues 354 - 364 (chain B) in PDB entry 3LMK
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 TRP 354 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B ARG* 6.3 0.2 - - - +
27B VAL* 3.1 44.5 + - + +
28B VAL 4.5 0.2 - - - -
29B ALA* 4.1 22.7 - - + -
43B VAL* 3.4 22.9 - - + -
44B HIS* 3.6 29.4 - + - -
60B VAL* 4.7 1.9 - - + +
66B ILE* 3.7 17.7 - - + -
69B VAL* 3.8 28.3 - - + -
95B ILE* 3.5 26.9 - - + -
96B ARG* 4.4 0.4 - - - -
97B ASP* 4.2 15.8 + - + +
352B ASN* 3.2 16.0 + - - +
353B PRO* 1.3 81.9 - - + +
355B PHE* 1.3 59.9 + - - +
356B GLN 3.4 2.2 - - - -
357B GLU* 3.4 18.8 + - - +
358B PHE* 2.9 27.4 + - - +
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Residues in contact with PHE 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ILE* 3.9 13.7 - - + -
341B TYR* 4.7 1.8 - + - -
344B LEU* 3.8 26.7 - - + -
345B ARG 3.8 4.9 - - - -
346B PRO* 3.7 32.1 - - + -
349B ASN* 3.2 37.2 - - + +
352B ASN* 3.2 33.7 + - - +
353B PRO 3.4 0.2 - - - -
354B TRP* 1.3 78.4 - - - +
356B GLN* 1.3 58.7 + - + +
358B PHE* 3.1 20.9 + + - +
359B TRP* 2.8 55.9 + + - +
387B LEU* 4.2 6.7 - - + -
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Residues in contact with GLN 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B PRO* 3.9 24.8 + - + +
349B ASN 5.4 3.7 - - - +
350B HIS* 5.8 4.3 - - - -
352B ASN 4.8 1.1 + - - +
353B PRO 5.1 3.8 + - - +
354B TRP 3.4 0.4 - - - -
355B PHE* 1.3 77.3 - - + +
357B GLU* 1.3 63.5 + - - +
359B TRP* 3.3 3.1 + - - +
360B GLN* 3.0 34.6 + - - +
367B LEU* 4.1 25.0 - - + +
369B GLY* 5.5 8.3 - - - -
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Residues in contact with GLU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B HIS* 3.0 40.5 + - - -
58B GLY 5.1 0.2 - - - +
59B ALA* 5.5 0.3 - - - -
60B VAL* 3.6 16.9 + - + +
353B PRO 5.4 1.5 + - - +
354B TRP* 3.4 21.0 + - - +
356B GLN* 1.3 79.2 - - - +
358B PHE* 1.3 61.9 + - - +
360B GLN* 3.4 11.7 + - - +
361B HIS* 3.0 22.5 + - + +
377B TYR* 4.9 0.9 + - - -
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Residues in contact with PHE 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B VAL* 3.8 21.7 - - + +
61B ARG 4.9 0.4 - - - -
62B GLU* 3.4 50.9 - - + -
66B ILE* 3.5 37.2 - - + -
341B TYR* 3.6 14.4 - - - -
354B TRP 2.9 11.2 + - - +
355B PHE* 3.4 24.7 - + - +
357B GLU* 1.3 72.7 - - - +
359B TRP* 1.3 67.5 + + - +
361B HIS* 3.1 3.4 + - + +
362B ARG* 2.8 44.0 + - + +
387B LEU* 3.7 20.9 - - + -
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Residues in contact with TRP 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B LEU 3.9 9.0 - - - -
345B ARG* 3.4 26.2 - - - -
346B PRO* 3.5 45.8 - - + +
347B GLU* 5.5 0.2 - - - -
355B PHE* 2.8 33.4 + + + +
356B GLN 3.7 4.3 - - - +
358B PHE* 1.3 75.9 - + - +
360B GLN* 1.3 62.0 + - - +
362B ARG* 4.5 1.6 - - - -
363B PHE* 3.2 62.8 + + - +
365B CYS* 4.6 0.2 - - - -
367B LEU* 3.9 18.0 - - + +
381B CYS* 4.3 6.0 - - - +
382B ASN 5.5 0.4 + - - -
385B LEU* 3.6 32.5 - - + +
386B THR* 4.4 0.9 - - - -
387B LEU* 3.6 35.0 - - + -
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Residues in contact with GLN 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B GLN* 3.0 23.2 + - - +
357B GLU* 3.7 8.7 - - - +
359B TRP* 1.3 76.9 - - - +
361B HIS* 1.3 59.8 + - - +
364B GLN* 2.9 24.4 + - - -
365B CYS* 3.2 28.7 + - - +
366B ARG* 3.6 4.8 - - - +
367B LEU* 2.8 49.7 + - + +
377B TYR* 3.5 18.2 - - + +
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Residues in contact with HIS 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ALA* 4.2 19.2 - - + +
60B VAL* 3.6 34.0 + - + +
357B GLU* 3.0 15.0 + - + +
358B PHE* 3.1 8.5 + - - +
360B GLN* 1.3 74.9 - - - +
362B ARG* 1.3 69.0 + - - +
363B PHE 3.2 0.9 + - - -
364B GLN* 2.9 35.0 + - - +
377B TYR* 3.4 16.1 + + - +
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Residues in contact with ARG 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLU* 3.3 31.6 + - - -
358B PHE* 2.8 36.4 + - + +
359B TRP 3.8 4.9 - - - +
361B HIS* 1.3 77.8 + - - +
363B PHE* 1.3 94.1 + - + +
364B GLN* 4.9 2.8 - - - +
387B LEU* 3.4 23.3 + - + +
389B THR* 2.8 29.3 + - - -
390B HIS* 3.9 27.4 + - - +
391B HIS* 4.3 3.0 + - - +
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Residues in contact with PHE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B TRP* 3.2 66.5 + + - -
361B HIS 3.2 0.6 - - - -
362B ARG* 1.3 112.3 - - + +
364B GLN* 1.3 72.1 + - - +
365B CYS* 3.3 21.9 + - - +
385B LEU* 3.6 27.1 - - + +
386B THR 3.7 32.5 - - - -
387B LEU* 4.4 7.4 - - + -
389B THR* 5.7 2.2 - - - -
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Residues in contact with GLN 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B GLN 2.9 9.0 + - - -
361B HIS* 2.9 31.2 + - - +
362B ARG 4.9 2.9 - - - +
363B PHE* 1.3 81.8 - - - +
365B CYS* 1.3 57.5 + - - +
377B TYR* 3.3 45.3 - - - +
378B ASN 4.9 0.5 + - - -
379B LYS* 4.5 10.0 + - - +
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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