Contacts of the helix formed by residues 3429 - 3449 (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 ASN3429 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3420F ASN* 4.4 9.0 + - - +
3423F HIS* 4.2 14.3 - - - +
3424F TRP* 3.9 30.9 - - - +
3427F GLU 4.3 2.2 + - - +
3428F PRO* 1.3 74.6 - - - +
3430F PRO* 1.3 68.8 - - + +
3431F SER* 4.5 2.2 - - - +
3432F ALA* 3.8 23.4 - - + +
3433F GLU* 3.2 20.6 + - - +
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Residues in contact with PRO3430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3428F PRO 3.4 10.3 - - - +
3429F ASN* 1.3 85.3 - - + +
3431F SER* 1.3 59.7 + - - +
3433F GLU* 3.4 7.2 + - + +
3434F GLU* 3.1 28.2 + - - +
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Residues in contact with SER3431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3429F ASN* 3.3 3.4 - - - +
3430F PRO* 1.3 80.3 - - - +
3432F ALA* 1.3 60.2 + - - +
3434F GLU* 3.4 6.2 + - - +
3435F LEU* 2.9 29.1 + - - +
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Residues in contact with ALA3432 (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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3429F ASN* 3.4 26.3 + - + +
3430F PRO 3.3 0.4 - - - -
3431F SER* 1.3 77.8 - - - +
3433F GLU* 1.3 59.6 + - - +
3435F LEU* 3.4 6.4 + - - +
3436F PHE* 3.0 28.4 + - - +
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Residues in contact with GLU3433 (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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3428F PRO* 6.6 0.2 - - + -
3429F ASN 3.2 15.9 + - - +
3430F PRO* 3.8 7.4 - - + +
3432F ALA* 1.3 77.8 - - - +
3434F GLU* 1.3 61.6 + - - +
3436F PHE* 3.4 8.2 + - - +
3437F ARG* 3.3 19.4 + - - +
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Residues in contact with GLU3434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3430F PRO 3.1 17.7 + - - +
3431F SER* 3.9 5.8 - - - +
3433F GLU* 1.3 74.3 - - - +
3435F LEU* 1.3 63.9 + - - +
3437F ARG* 3.3 9.0 + - - +
3438F MET* 3.3 18.9 + - - +
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Residues in contact with LEU3435 (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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3431F SER 2.9 18.3 + - - +
3432F ALA* 3.8 7.6 - - - +
3433F GLU 3.3 0.2 - - - -
3434F GLU* 1.3 77.6 - - - +
3436F PHE* 1.3 61.5 + - - +
3438F MET* 3.3 8.5 + - - +
3439F VAL* 3.1 21.8 + - - +
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Residues in contact with PHE3436 (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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3432F ALA 3.0 17.0 + - - +
3433F GLU* 3.7 8.1 - - - +
3434F GLU 3.3 0.2 - - - -
3435F LEU* 1.3 78.6 - - - +
3437F ARG* 1.3 56.6 + - - +
3439F VAL* 3.4 7.4 + - - +
3440F GLY* 3.0 23.9 + - - -
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Residues in contact with ARG3437 (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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3433F GLU 3.3 10.5 + - - +
3434F GLU* 3.6 10.8 - - - +
3435F LEU 3.3 0.2 - - - -
3436F PHE* 1.3 77.6 - - - +
3438F MET* 1.3 63.2 + - - +
3440F GLY* 3.2 10.7 + - - -
3441F GLU* 3.3 11.4 + - - +
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Residues in contact with MET3438 (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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3434F GLU 3.3 10.7 + - - +
3435F LEU* 3.7 11.0 - - - +
3436F PHE 3.3 0.2 - - - -
3437F ARG* 1.3 80.6 - - - +
3439F VAL* 1.3 59.9 + - - +
3441F GLU* 3.3 18.9 + - - +
3442F ILE* 3.7 6.4 + - - +
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Residues in contact with VAL3439 (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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3435F LEU 3.1 13.3 + - - +
3436F PHE* 3.8 9.4 - - - +
3438F MET* 1.3 75.4 - - - +
3440F GLY* 1.3 60.7 + - - +
3442F ILE* 3.3 8.6 + - - +
3443F PHE* 3.0 25.3 + - - +
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Residues in contact with GLY3440 (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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3436F PHE 3.0 14.6 + - - -
3437F ARG* 3.2 6.0 + - - -
3438F MET 3.2 0.8 - - - -
3439F VAL* 1.3 76.2 - - - +
3441F GLU* 1.3 63.3 + - - +
3443F PHE* 3.2 16.7 + - - +
3444F ILE* 3.3 13.0 + - - +
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Residues in contact with GLU3441 (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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3437F ARG 3.3 9.1 + - - +
3438F MET* 3.3 12.6 + - - +
3439F VAL 3.2 0.8 - - - -
3440F GLY* 1.3 77.4 - - - +
3442F ILE* 1.3 60.1 + - - +
3444F ILE* 3.3 18.7 + - - +
3445F TYR* 3.8 5.7 + - - +
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Residues in contact with ILE3442 (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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3438F MET 3.7 7.1 + - - +
3439F VAL* 3.3 10.0 + - - +
3440F GLY 3.3 0.4 - - - -
3441F GLU* 1.3 77.1 - - - +
3443F PHE* 1.3 59.2 + - - +
3445F TYR* 3.3 8.1 + - - +
3446F TRP* 2.9 33.5 + - + +
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Residues in contact with PHE3443 (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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3439F VAL 3.0 14.3 + - - +
3440F GLY* 3.5 13.9 - - - +
3441F GLU 3.2 0.2 - - - -
3442F ILE* 1.3 76.7 - - - +
3444F ILE* 1.3 64.6 + - - +
3446F TRP* 3.3 22.1 + - + +
3447F SER* 4.0 4.9 + - - -
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Residues in contact with ILE3444 (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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3440F GLY 3.3 9.7 + - - +
3441F GLU* 3.6 12.6 - - - +
3442F ILE 3.2 0.8 - - - -
3443F PHE* 1.3 78.9 - - - +
3445F TYR* 1.3 57.0 + - - +
3446F TRP 3.7 0.2 + - - -
3447F SER* 4.3 0.7 + - - -
3448F LYS* 3.3 22.7 + - - +
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Residues in contact with TYR3445 (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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3441F GLU 3.8 5.9 + - - +
3442F ILE* 3.3 10.9 + - - +
3444F ILE* 1.3 76.5 - - - +
3446F TRP* 1.3 64.1 + - - +
3447F SER 3.4 1.1 - - - -
3448F LYS* 4.0 9.2 - - - -
3449F LYS* 3.4 28.4 + - + +
3452F PHE* 4.5 16.8 - - + +
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Residues in contact with TRP3446 (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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3442F ILE* 2.9 18.7 + - + +
3443F PHE* 3.3 19.6 + - + +
3445F TYR* 1.3 80.0 - - - +
3447F SER* 1.3 64.3 + - - +
3449F LYS 3.7 2.3 - - - +
3452F PHE* 5.8 2.9 - - + -
3453F LYS* 3.3 44.4 - - + +
3456F GLU* 4.3 25.8 - - + -
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Residues in contact with SER3447 (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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3443F PHE 4.0 5.9 + - - -
3444F ILE 4.3 0.4 + - - -
3446F TRP* 1.3 83.6 - - - +
3448F LYS* 1.3 65.4 + - - +
3449F LYS 3.4 3.2 - - - -
3450F HIS* 4.7 3.1 + - - +
3453F LYS* 5.5 0.4 - - - -
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Residues in contact with LYS3448 (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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3444F ILE 3.3 21.8 + - - +
3445F TYR* 4.3 4.3 - - - -
3446F TRP 3.7 0.2 - - - -
3447F SER* 1.3 80.5 - - - +
3449F LYS* 1.3 59.5 + - + +
3450F HIS* 3.6 3.3 + - - +
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Residues in contact with LYS3449 (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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3445F TYR* 3.4 19.2 + - + +
3446F TRP 3.7 9.4 - - - +
3447F SER 4.5 2.0 - - - -
3448F LYS* 1.3 76.9 - - + +
3450F HIS* 1.3 63.9 + - - +
3451F ASN* 3.2 3.7 + - + +
3452F PHE* 3.4 34.1 + - + +
3453F LYS 3.5 8.1 + - - -
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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