Contacts of the helix formed by residues 391 - 409 (chain I) in PDB entry 5LN3
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 SER 391 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227I PRO* 5.9 2.6 - - - +
230I THR* 3.3 27.9 - - - +
356I PRO* 3.4 22.3 - - - +
390I LEU* 1.4 75.2 - - - +
392I GLY* 1.4 67.9 + - - +
393I ALA* 3.3 2.4 + - - -
394I ASP* 3.1 18.4 + - - +
395I ILE* 3.3 14.0 - - - +
307J ARG* 4.6 7.6 + - - -
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Residues in contact with GLY 392 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230I THR* 3.3 7.6 + - - -
364I ILE* 4.1 18.6 - - - -
368I HIS* 4.2 0.9 - - - -
391I SER* 1.4 76.9 - - - +
393I ALA* 1.3 50.0 + - - +
395I ILE* 3.1 13.0 + - - +
396I LYS* 2.7 49.8 + - - +
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Residues in contact with ALA 393 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229I GLY 5.2 2.5 - - - +
230I THR* 3.3 22.1 + - - +
391I SER* 5.0 0.4 - - - -
392I GLY* 1.3 72.6 - - - +
394I ASP* 1.4 62.1 + - - +
396I LYS* 3.3 15.5 + - + +
397I ALA* 2.9 28.6 + - - +
307J ARG* 4.0 21.1 - - - +
308J PRO* 4.2 12.8 - - - +
309J GLY* 5.2 6.0 - - - -
310J ARG* 5.9 0.4 - - - +
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Residues in contact with ASP 394 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390I LEU* 3.3 31.9 - - + +
391I SER* 3.1 29.9 + - - +
393I ALA* 1.4 60.0 - - - +
395I ILE* 1.3 58.2 + - - +
397I ALA* 3.3 7.6 + - - +
398I ILE* 2.8 38.8 + - + +
426I VAL* 4.3 14.1 - - + +
307J ARG* 4.9 4.4 + - - -
308J PRO* 3.4 31.2 - - - +
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Residues in contact with ILE 395 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361I LYS* 4.5 22.9 - - + +
364I ILE* 4.4 9.0 - - + -
365I PHE* 3.8 34.1 - - + -
368I HIS* 3.9 13.9 - - + +
384I ILE* 5.5 2.0 - - + -
387I LYS* 4.4 23.1 - - + +
390I LEU* 3.6 17.3 - - + +
391I SER 3.3 21.1 - - - +
392I GLY* 3.1 11.4 + - - +
394I ASP* 1.3 83.8 - - + +
396I LYS* 1.4 61.1 + - - +
398I ILE* 3.1 16.9 + - + +
399I CYS* 3.5 14.3 + - - -
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Residues in contact with LYS 396 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I ILE* 4.9 6.6 - - - +
230I THR 4.6 0.8 + - - -
234I LEU* 3.8 37.8 - - - +
364I ILE* 5.0 1.0 - - - +
368I HIS* 3.7 37.6 + - + +
392I GLY* 2.7 33.3 + - - +
393I ALA* 3.6 12.8 - - + +
395I ILE* 1.4 73.4 - - - +
397I ALA* 1.3 54.5 + - - +
399I CYS* 3.7 6.5 + - - +
400I THR* 2.6 30.1 + - - -
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Residues in contact with ALA 397 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393I ALA 2.9 17.9 + - - +
394I ASP* 3.3 10.1 - - - +
396I LYS* 1.3 76.0 - - - +
398I ILE* 1.4 65.9 + - + +
400I THR* 3.1 9.1 + - - -
401I GLU* 3.0 24.8 + - - +
426I VAL* 5.7 4.7 - - + -
308J PRO* 5.4 4.3 - - + -
309J GLY* 5.1 14.6 - - - +
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Residues in contact with ILE 398 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365I PHE* 5.8 4.0 - - + -
383I LEU* 6.5 0.4 - - + -
387I LYS* 3.5 40.4 - - - +
390I LEU* 4.8 4.5 - - + -
394I ASP* 2.8 29.1 + - + +
395I ILE* 3.1 7.3 + - + +
397I ALA* 1.4 73.0 - - - +
399I CYS* 1.4 61.7 - - - +
401I GLU* 3.3 7.7 - - - +
402I ALA* 3.1 27.4 + - - +
419I PHE* 4.9 15.0 - - + +
422I SER* 3.4 22.9 + - - +
423I LYS* 4.6 10.3 - - + +
426I VAL* 3.6 38.6 - - + -
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Residues in contact with CYS 399 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365I PHE* 4.2 22.4 - - - -
368I HIS* 4.1 29.6 - - + +
369I THR* 5.0 4.0 - - - -
372I MET* 5.0 19.8 - - + +
395I ILE 3.5 15.3 - - - -
396I LYS 3.9 6.7 - - - +
397I ALA 3.3 0.2 - - - -
398I ILE* 1.4 80.6 - - - +
400I THR* 1.3 52.6 + - - +
402I ALA* 3.6 6.5 + - - +
403I GLY* 2.8 29.5 + - - -
419I PHE* 5.2 10.7 - - + -
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Residues in contact with THR 400 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371I ARG* 5.6 3.3 + - - -
372I MET* 6.3 0.4 - - - -
396I LYS 2.6 23.4 + - - -
397I ALA* 3.3 11.5 - - - -
399I CYS* 1.3 72.4 - - - +
401I GLU* 1.3 63.2 + - - +
403I GLY 3.3 0.3 + - - -
404I LEU* 3.1 19.9 + - - +
180J ILE* 3.3 36.3 - - + +
181J ALA* 4.5 13.7 + - + +
313J ARG* 4.3 21.1 + - - +
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Residues in contact with GLU 401 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397I ALA 3.0 10.3 + - - +
398I ILE* 3.3 10.7 - - - +
400I THR* 1.3 75.3 - - - +
402I ALA* 1.3 64.2 + - - +
404I LEU* 3.2 19.5 + - + +
405I MET* 3.3 24.4 + - + +
422I SER* 3.5 34.7 - - - +
425I ASN* 3.4 27.2 + - - +
426I VAL* 3.8 13.3 - - - +
429I LYS* 4.8 5.0 + - - -
313J ARG* 5.2 11.6 - - - +
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Residues in contact with ALA 402 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398I ILE 3.1 13.6 + - - +
399I CYS 3.6 5.8 - - - +
401I GLU* 1.3 77.1 - - - +
403I GLY* 1.4 63.1 + - - +
405I MET* 2.9 28.6 + - - +
406I ALA* 3.3 7.5 + - - +
414I VAL* 5.3 4.3 - - + -
418I ASP* 4.1 20.8 - - + +
419I PHE* 4.2 24.2 - - + -
422I SER* 3.3 12.2 + - - +
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Residues in contact with GLY 403 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372I MET* 4.1 21.8 - - - -
399I CYS 2.8 17.9 + - - -
400I THR 3.3 3.7 + - - -
401I GLU 3.2 0.6 - - - -
402I ALA* 1.4 77.3 - - - +
404I LEU* 1.4 58.6 + - - +
406I ALA* 3.4 7.9 + - - +
407I LEU* 3.3 21.7 + - - +
414I VAL* 6.3 1.3 - - - -
178J LEU* 3.5 6.6 - - - +
180J ILE* 4.1 11.9 - - - -
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Residues in contact with LEU 404 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400I THR 3.1 11.1 + - - +
401I GLU* 3.2 13.4 + - + +
403I GLY* 1.4 73.5 - - - +
405I MET* 1.4 63.7 + - + +
407I LEU* 3.3 14.3 - - + +
408I ARG* 3.2 28.4 + - - +
163J GLU* 3.7 31.7 - - - +
164J VAL* 5.2 7.4 - - + +
168J PRO* 6.5 0.2 - - + -
175J PHE* 4.6 21.5 - - + -
180J ILE* 3.9 6.0 - - + +
183J PRO* 6.0 2.2 - - + -
313J ARG* 3.6 39.7 - - - +
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Residues in contact with MET 405 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401I GLU* 3.4 24.5 - - + +
402I ALA* 2.9 12.7 + - - +
404I LEU* 1.4 74.4 - - + +
406I ALA* 1.4 62.4 + - - +
408I ARG* 3.3 39.4 + - - +
409I GLU* 3.1 24.5 - - + +
418I ASP* 3.8 33.4 - - - +
421I LYS* 4.0 31.4 - - + -
422I SER* 3.7 18.6 - - - +
425I ASN* 4.7 7.6 - - - +
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Residues in contact with ALA 406 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372I MET* 5.9 2.0 - - + -
402I ALA 3.3 6.4 + - - +
403I GLY* 3.5 12.8 - - - +
404I LEU 3.2 0.2 - - - -
405I MET* 1.4 79.3 - - - +
407I LEU* 1.3 58.3 - - - +
409I GLU* 3.3 14.4 + - - +
410I ARG 3.1 19.6 + - - -
411I ARG* 3.1 25.4 + - - +
412I MET* 5.6 0.4 - - - -
413I LYS 4.5 11.9 - - - +
414I VAL* 5.6 4.5 - - + -
418I ASP* 4.3 14.8 - - - +
178J LEU* 5.3 5.8 - - + -
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Residues in contact with LEU 407 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403I GLY 3.3 8.9 + - - +
404I LEU* 3.3 22.0 - - + +
406I ALA* 1.3 75.9 - - - +
408I ARG* 1.4 59.6 + - - +
410I ARG* 3.0 24.6 + - - +
411I ARG 4.5 3.6 - - - -
163J GLU* 6.1 0.4 - - - +
174J LEU* 4.8 23.8 - - + +
175J PHE* 3.5 43.7 - - + -
178J LEU* 4.0 22.9 - - + +
180J ILE* 5.2 1.3 - - + -
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Residues in contact with ARG 408 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404I LEU* 3.2 19.7 + - - +
405I MET* 3.3 46.4 + - - +
407I LEU* 1.4 70.6 - - - +
409I GLU* 1.4 71.0 + - - +
410I ARG* 3.1 15.2 + - - +
163J GLU* 5.3 22.1 + - + +
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Residues in contact with GLU 409 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C LYS* 5.8 3.8 - - - +
405I MET* 3.1 23.6 - - + +
406I ALA* 3.3 11.8 + - - +
408I ARG* 1.4 92.1 + - - +
410I ARG* 1.4 68.6 + - - +
411I ARG* 3.4 44.3 + - + +
418I ASP* 5.9 0.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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