Contacts of the helix formed by residues 4663 - 4681 (chain F) in PDB entry 6X34
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 LYS4663 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4659F TYR* 3.4 39.8 + - + +
4662F LEU* 1.3 86.2 - - + +
4664F VAL* 1.3 62.4 + - - +
4665F PRO 3.4 2.0 - - - -
4666F LEU* 2.9 17.0 + - + +
4667F VAL* 2.9 33.5 + - + +
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Residues in contact with VAL4664 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4659F TYR* 3.2 35.4 - - + +
4660F ASN* 3.5 31.4 - - - +
4663F LYS* 1.3 76.2 - - - +
4665F PRO* 1.3 63.2 - - - +
4667F VAL* 3.2 7.2 - - + +
4668F ILE* 3.1 33.9 + - + +
4781F ILE* 3.6 40.4 - - + -
4787F PHE* 4.9 2.7 - - + -
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Residues in contact with PRO4665 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4238F PHE* 3.2 36.9 - - + -
4660F ASN 3.3 19.7 - - - +
4661F CYS* 4.2 11.0 - - - +
4662F LEU 4.1 5.4 - - - +
4663F LYS 3.7 7.9 - - - +
4664F VAL* 1.3 89.6 - - + +
4666F LEU* 1.3 55.9 + - - +
4668F ILE* 4.0 7.1 - - + +
4669F PHE* 3.2 18.5 + - - +
4712F ASN* 4.4 7.7 - - - +
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Residues in contact with LEU4666 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4235F ASP* 3.9 33.9 - - + +
4238F PHE* 4.5 6.7 - - + -
4239F GLU* 5.6 11.2 - - + -
4662F LEU 4.6 5.6 + - - +
4663F LYS* 2.9 23.9 + - + +
4665F PRO* 1.3 77.5 - - - +
4667F VAL* 1.3 65.5 + - + +
4669F PHE* 3.2 7.0 + - + -
4670F LYS* 2.7 33.2 + - + +
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Residues in contact with VAL4667 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4659F TYR* 5.2 6.3 - - + +
4663F LYS* 2.9 16.5 + - + +
4664F VAL* 3.2 22.9 - - + +
4666F LEU* 1.3 80.0 - - + +
4668F ILE* 1.3 62.3 + - + +
4670F LYS* 3.9 7.5 - - - +
4671F ARG* 3.2 24.4 + - - +
4780F VAL* 5.6 6.6 - - + +
4781F ILE* 4.2 17.3 - - + -
4784F ASP* 5.8 6.5 - - + -
4786F SER* 4.7 14.4 - - - +
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Residues in contact with ILE4668 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4664F VAL* 3.1 22.6 + - + +
4665F PRO* 4.2 5.8 - - + +
4667F VAL* 1.3 78.3 - - - +
4669F PHE* 1.3 57.2 + - - +
4671F ARG* 3.3 4.3 + - + +
4672F GLU* 2.8 30.4 + - + +
4710F PRO* 5.0 6.1 - - + -
4712F ASN* 3.8 27.4 - - + +
4773F TYR* 5.5 3.6 - - + +
4776F TRP* 4.7 25.1 - - + -
4777F LYS* 4.4 16.2 - - + +
4780F VAL* 4.9 10.5 - - + -
4781F ILE* 3.8 26.9 - - + -
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Residues in contact with PHE4669 (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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4231F SER 5.6 0.4 - - - -
4234F GLU* 3.5 41.1 - - + -
4235F ASP* 4.1 10.8 - - + -
4238F PHE* 4.1 21.8 - + + -
4665F PRO 3.2 18.6 + - - +
4666F LEU* 3.8 5.4 - - + +
4668F ILE* 1.3 79.4 - - - +
4670F LYS* 1.3 61.1 + - - +
4672F GLU* 4.4 4.5 - - + +
4673F LYS* 3.0 36.1 + - + +
4712F ASN* 3.2 34.5 - - + -
4713F TYR* 3.8 29.2 - + + -
4714F TRP* 4.2 20.0 - + - -
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Residues in contact with LYS4670 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4235F ASP* 6.5 0.4 - - + -
4666F LEU* 2.7 27.5 + - + +
4667F VAL* 3.9 10.8 - - + +
4668F ILE 3.3 0.2 - - - -
4669F PHE* 1.3 76.0 - - - +
4671F ARG* 1.3 59.6 + - - +
4673F LYS* 4.3 3.2 - - - +
4674F GLU* 3.8 17.5 + - - +
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Residues in contact with ARG4671 (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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4667F VAL 3.2 16.1 + - - +
4668F ILE* 3.9 4.7 - - + +
4669F PHE 3.2 0.4 - - - -
4670F LYS* 1.3 76.5 - - - +
4672F GLU* 1.3 59.5 + - - +
4673F LYS 3.2 1.8 - - - -
4674F GLU* 3.3 6.5 + - + +
4675F LEU* 3.0 27.9 + - + +
4696F LYS* 4.1 29.5 + - - +
4700F ASP* 5.9 4.8 - - - +
4776F TRP* 3.9 29.8 - - + +
4780F VAL* 3.4 38.7 - - - +
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Residues in contact with GLU4672 (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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4668F ILE* 2.8 27.7 + - + +
4669F PHE* 4.3 4.9 - - - +
4671F ARG* 1.3 73.9 - - - +
4673F LYS* 1.3 56.7 + - - +
4675F LEU* 3.4 8.9 + - + +
4676F ALA* 2.9 30.5 + - - +
4709F PHE* 6.3 2.0 - - + -
4710F PRO* 5.4 13.2 - - + +
4712F ASN* 5.6 2.2 - - + -
4713F TYR* 4.4 19.1 - - + +
4776F TRP* 5.1 11.3 - - + -
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Residues in contact with LYS4673 (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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4231F SER* 5.3 8.5 - - - +
4669F PHE* 3.0 29.6 + - + +
4670F LYS* 4.5 4.3 - - - +
4672F GLU* 1.3 77.4 - - - +
4674F GLU* 1.3 57.8 + - - +
4676F ALA* 4.0 1.0 - - - +
4677F ARG* 3.0 29.1 + - - +
4713F TYR* 3.6 28.7 + - + -
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Residues in contact with GLU4674 (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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4670F LYS 3.8 13.0 + - - +
4671F ARG* 3.3 11.8 + - + +
4673F LYS* 1.3 77.0 - - - +
4675F LEU* 1.3 59.4 + - - +
4677F ARG* 3.7 4.4 + - - +
4678F LYS* 3.0 28.2 + - - +
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Residues in contact with LEU4675 (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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4671F ARG* 3.0 20.1 + - + +
4672F GLU* 3.8 7.9 - - + +
4674F GLU* 1.3 75.0 - - - +
4676F ALA* 1.3 63.7 + - - +
4678F LYS* 3.2 6.7 + - + +
4679F LEU* 3.2 32.9 + - + +
4684F LEU* 3.9 28.0 - - + -
4700F ASP* 4.6 15.0 - - + -
4703F VAL* 3.7 27.8 - - + -
4704F LEU* 4.7 5.6 - - + -
4709F PHE* 3.7 27.1 - - + -
4776F TRP* 4.9 9.0 - - + -
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Residues in contact with ALA4676 (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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4672F GLU 2.9 17.9 + - - +
4673F LYS 4.0 1.1 - - - +
4675F LEU* 1.3 78.3 - - - +
4677F ARG* 1.3 60.7 + - - +
4679F LEU* 3.4 12.8 + - - +
4680F GLU* 3.7 9.2 + - - +
4709F PHE* 6.0 3.8 - - + -
4713F TYR* 4.0 33.9 - - + +
4718F VAL* 3.9 30.2 - - + +
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Residues in contact with ARG4677 (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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4673F LYS 3.0 18.7 + - - +
4674F GLU* 4.1 5.6 - - - +
4676F ALA* 1.3 75.7 - - - +
4678F LYS* 1.3 61.7 + - - +
4680F GLU* 3.6 8.0 + - - +
4681F PHE* 3.4 20.1 + - - +
4713F TYR* 5.3 3.1 + - - +
5017F TRP* 6.4 2.2 - - + -
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Residues in contact with LYS4678 (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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4674F GLU 3.0 18.3 + - - +
4675F LEU* 3.2 12.9 + - + +
4677F ARG* 1.3 76.2 - - - +
4679F LEU* 1.3 62.8 + - + +
4681F PHE* 2.8 27.4 - - - +
4682F ASP 3.4 7.7 - - - +
4683F GLY* 3.3 14.8 - - - -
4684F LEU* 5.5 3.8 - - + +
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Residues in contact with LEU4679 (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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4675F LEU* 3.2 38.6 + - + +
4676F ALA* 3.7 9.4 - - - +
4677F ARG 3.3 0.6 - - - -
4678F LYS* 1.3 77.8 - - - +
4680F GLU* 1.3 64.3 + - - +
4681F PHE 3.2 6.8 - - - +
4683F GLY* 4.8 5.3 + - - -
4684F LEU* 4.5 13.2 - - + -
4686F ILE* 5.9 0.3 - - - +
4704F LEU* 5.1 7.6 - - + -
4709F PHE* 4.1 20.9 - - + -
4718F VAL* 4.0 30.1 - - + +
4719F LYS* 4.8 5.8 - - + -
4722F VAL* 3.7 37.0 - - + +
4726F HIS* 4.9 2.1 - - - -
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Residues in contact with GLU4680 (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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4676F ALA 3.7 6.7 + - - +
4677F ARG* 3.6 10.6 + - - +
4678F LYS 3.4 0.4 - - - -
4679F LEU* 1.3 79.7 - - - +
4681F PHE* 1.3 59.6 + - - +
4718F VAL* 5.8 0.2 - - - +
4721F LYS* 6.4 2.0 - - + -
4722F VAL* 5.7 3.4 - - - +
4725F LYS* 5.3 6.1 - - - +
4726F HIS* 4.3 12.1 + - - -
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Residues in contact with PHE4681 (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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4677F ARG 3.4 14.4 + - - +
4678F LYS* 2.8 14.8 - - - +
4679F LEU 3.2 10.4 - - - +
4680F GLU* 1.3 78.6 - - - +
4682F ASP* 1.3 65.9 + - - +
4683F GLY 3.0 2.8 + - - -
4686F ILE* 5.0 0.2 - - - +
4726F HIS* 4.1 11.2 + - - -
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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
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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