Contacts of the helix formed by residues 503 - 519 (chain F) in PDB entry 3CB4
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 ASN 503 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B LYS 4.6 0.2 - - - -
424F GLU* 6.2 0.2 - - - -
500F HIS* 3.5 5.4 + - - -
501F ARG 3.2 0.2 - - - -
502F ASP* 1.3 88.9 + - - +
504F SER* 1.3 55.0 + - - +
505F GLN 3.3 2.0 - - - +
506F ASN* 3.5 30.7 + - + +
507F ARG* 2.7 67.4 + - - +
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Residues in contact with SER 504 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LYS 3.5 3.8 + - - -
165B THR* 3.5 16.3 - - - +
481F VAL* 3.4 27.9 - - - +
483F VAL* 4.1 5.3 - - - +
499F THR* 3.7 16.2 - - - -
500F HIS 3.3 4.4 + - - -
501F ARG 2.6 21.3 + - - -
503F ASN* 1.3 74.4 - - - +
505F GLN* 1.3 62.6 + - - +
507F ARG* 3.8 1.2 - - - +
508F GLY* 3.0 22.7 + - - -
532F ILE* 4.3 7.4 - - - -
537F ILE* 3.4 12.0 - - - +
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Residues in contact with GLN 505 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B SER* 6.6 0.2 - - - -
23B ARG* 3.2 33.6 + - + +
26B GLN* 3.8 24.4 - - - +
27B ILE* 5.6 1.2 - - - +
163B ALA 4.2 8.0 + - - +
164B LYS 3.2 18.8 + - - +
165B THR 3.4 15.7 + - - +
166B GLY* 3.4 19.6 + - - -
169B VAL* 5.4 0.2 - - - +
504F SER* 1.3 82.5 + - - +
506F ASN* 1.3 62.3 + - + +
508F GLY* 3.2 2.8 + - - -
509F ARG* 3.2 19.6 + - - +
537F ILE* 2.8 31.5 + - - +
538F ALA* 4.8 0.5 - - - +
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Residues in contact with ASN 506 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLN* 4.9 2.5 - - - +
503F ASN* 3.3 36.6 + - + +
504F SER 3.2 0.4 - - - -
505F GLN* 1.3 84.2 - - + +
507F ARG* 1.3 62.7 + - - +
509F ARG* 3.3 26.5 + - - +
510F GLU* 2.8 47.5 + - - +
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Residues in contact with ARG 507 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425F LYS* 5.4 4.4 - - - +
426F ARG* 5.4 1.0 - - - +
449F GLU* 3.2 38.6 + - - -
452F LEU* 5.9 8.0 - - + +
497F LEU* 4.6 17.7 - - + +
499F THR* 3.7 33.3 + - + +
500F HIS* 4.7 8.7 + - - +
503F ASN* 2.7 58.0 + - - +
504F SER 4.0 4.7 - - - +
505F GLN 3.3 0.2 - - - -
506F ASN* 1.3 71.1 - - - +
508F GLY* 1.3 59.5 + - - +
510F GLU* 3.5 26.0 + - - +
511F LEU* 3.1 29.2 + - - +
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Residues in contact with GLY 508 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483F VAL* 4.5 6.0 - - - +
504F SER 3.0 14.4 + - - -
505F GLN 3.2 4.6 + - - -
507F ARG* 1.3 76.4 - - - +
509F ARG* 1.3 61.9 + - - +
511F LEU* 3.3 5.3 + - - +
512F VAL* 3.2 27.4 + - - +
530F ALA* 3.9 18.8 - - - +
537F ILE* 3.9 6.7 - - - -
538F ALA* 4.0 6.5 - - - -
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Residues in contact with ARG 509 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLN* 3.3 48.9 + - + +
30B GLY 5.5 7.0 - - - -
505F GLN 3.2 7.1 + - - +
506F ASN* 3.3 25.7 + - - +
508F GLY* 1.3 75.2 - - - +
510F GLU* 1.3 80.9 + - - +
512F VAL* 3.3 5.6 + - - +
513F GLU* 3.1 50.8 + - - +
538F ALA* 4.1 11.7 - - + +
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Residues in contact with GLU 510 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506F ASN* 2.8 34.0 + - - +
507F ARG* 3.8 25.6 - - + +
508F GLY 3.3 0.2 - - - -
509F ARG* 1.3 90.9 + - - +
511F LEU* 1.3 60.9 + - - +
513F GLU* 3.4 5.3 + - - +
514F LYS* 3.0 29.8 + - - +
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Residues in contact with LEU 511 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367F ALA* 6.2 2.2 - - + -
483F VAL* 4.7 9.0 - - + +
485F VAL* 3.6 27.6 - - + -
495F LEU* 3.4 39.9 - - + +
497F LEU* 3.6 31.9 - - + -
507F ARG 3.1 15.1 + - - +
508F GLY* 3.3 7.1 + - - +
510F GLU* 1.3 76.7 - - - +
512F VAL* 1.3 62.1 + - + +
514F LYS* 3.6 13.5 + - + +
515F MET* 3.2 28.5 + - + +
530F ALA* 5.2 1.8 - - + -
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Residues in contact with VAL 512 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485F VAL* 6.5 0.2 - - + -
508F GLY 3.2 14.2 + - - +
509F ARG* 3.7 7.2 - - + +
510F GLU 3.3 0.2 - - - -
511F LEU* 1.3 75.2 - - + +
513F GLU* 1.3 64.6 + - - +
515F MET* 3.2 4.3 + - - +
516F LYS* 2.9 28.1 + - + +
528F ILE* 4.0 23.8 - - + +
530F ALA* 4.0 13.2 - - + +
538F ALA* 3.8 29.4 - - + +
539F ARG 4.5 1.1 - - - -
540F SER* 3.4 37.5 - - - +
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Residues in contact with GLU 513 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLY* 4.9 12.3 - - - -
509F ARG* 3.1 42.0 + - - +
510F GLU* 3.8 7.6 - - - +
512F VAL* 1.3 78.6 - - - +
514F LYS* 1.3 64.9 + - - +
516F LYS* 3.1 33.5 + - - +
517F ASP* 3.0 30.9 + - - +
540F SER* 5.0 1.4 + - - -
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Residues in contact with LYS 514 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365F THR 4.5 13.7 + - - +
366F THR* 4.6 1.7 - - - -
367F ALA* 3.9 33.9 - - + +
368F PRO* 5.6 0.6 - - - +
452F LEU* 5.8 2.0 - - - +
510F GLU 3.0 17.7 + - - +
511F LEU* 3.7 16.2 - - + +
512F VAL 3.4 0.2 - - - -
513F GLU* 1.3 76.6 - - - +
515F MET* 1.3 66.9 + - - +
517F ASP* 3.4 12.8 + - - +
518F LEU* 3.4 32.8 + - + +
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Residues in contact with MET 515 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333F ALA* 6.2 0.4 - - + -
334F LEU* 4.5 18.6 - - + -
485F VAL* 5.3 0.4 - - + -
487F ILE* 5.1 5.8 - - + -
495F LEU* 3.7 41.3 - - + -
511F LEU* 3.2 21.8 + - + +
512F VAL 3.4 7.9 - - - +
513F GLU 3.2 0.2 - - - -
514F LYS* 1.3 79.0 - - - +
516F LYS* 1.3 57.5 + - - +
517F ASP 3.1 1.6 - - - -
518F LEU* 2.8 38.3 + - + +
519F ILE* 3.0 37.7 + - + +
528F ILE* 3.7 31.2 - - + -
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Residues in contact with LYS 516 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLY 5.3 0.4 - - - -
30B GLY* 5.8 2.4 - - - -
512F VAL 2.9 18.1 + - - +
513F GLU* 3.1 40.3 + - - +
515F MET* 1.3 72.3 - - - +
517F ASP* 1.3 59.4 + - - +
518F LEU 3.4 0.2 - - - -
519F ILE 3.2 20.6 - - - +
520F PRO* 5.2 0.2 - - - +
528F ILE* 4.0 9.2 - - + +
540F SER* 3.1 33.0 + - - +
541F THR 5.3 1.8 - - - +
542F VAL* 3.9 28.5 - - + +
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Residues in contact with ASP 517 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C ASP* 5.0 7.4 - - - +
553C CYS* 4.5 9.5 - - - +
513F GLU* 3.0 21.5 + - - +
514F LYS* 3.6 11.5 - - - +
515F MET 3.1 0.6 - - - -
516F LYS* 1.3 78.3 - - - +
518F LEU* 1.3 69.9 + - + +
519F ILE 3.4 1.3 + - - -
520F PRO* 5.3 0.3 - - - +
553F CYS* 5.4 2.6 - - - -
554F TYR* 5.4 5.7 - - - -
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Residues in contact with LEU 518 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552C LYS* 3.3 10.2 - - + +
553C CYS 3.0 46.8 + - - +
555C GLY* 4.2 20.0 - - - +
334F LEU* 6.0 0.4 - - + -
364F ILE* 3.9 35.0 - - + -
365F THR 5.6 4.0 - - - +
514F LYS* 3.4 26.7 + - + +
515F MET* 2.8 21.9 + - + +
517F ASP* 1.3 85.3 - - + +
519F ILE* 1.3 63.6 + - + +
520F PRO* 4.1 1.3 - - - -
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Residues in contact with ILE 519 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550C LEU* 4.8 7.4 - - + -
551C ALA 4.1 5.6 - - - +
552C LYS* 5.4 4.9 - - + -
333F ALA* 5.9 0.7 - - + -
334F LEU* 6.2 0.9 - - + -
487F ILE* 3.8 23.8 - - + -
515F MET* 3.0 40.9 + - + +
516F LYS 3.2 15.8 - - - +
517F ASP 3.4 1.7 - - - -
518F LEU* 1.3 86.6 - - + +
520F PRO* 1.4 64.3 - - - +
522F GLN* 3.2 22.0 - - - +
526F ILE* 3.7 22.7 - - + -
528F ILE* 4.1 12.8 - - + -
542F VAL* 3.6 17.2 - - + +
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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
------------------------------------------------------------
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