Contacts of the helix formed by residues 6839 - 6853 (chain A) in PDB entry 6W75
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 MET6839 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6834A LEU* 4.5 0.4 - - - -
6837A GLY 3.8 4.9 + - - +
6838A ILE* 1.3 78.7 - - - +
6840A MET* 1.3 66.2 + - - +
6841A ASN* 4.2 5.4 - - + +
6842A VAL* 3.0 22.7 + - + +
6843A ALA* 3.1 10.2 + - - +
6874A LYS* 3.9 21.3 - - + +
6876A VAL* 4.5 0.2 - - + -
6878A PRO* 3.7 30.1 - - + -
7107A FMT 3.7 19.1 - - - +
4293B ASN* 3.5 39.9 - - - +
4294B CYS 3.6 17.0 - - - +
4295B VAL* 4.2 13.2 - - + -
4296B LYS 5.2 2.8 + - - +
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Residues in contact with MET6840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6831A SER* 6.5 1.1 - - - -
6832A ALA* 6.1 2.2 - - + +
6834A LEU* 4.0 26.4 - - + +
6838A ILE 3.9 0.4 + - - -
6839A MET* 1.3 72.2 - - - +
6841A ASN* 1.3 68.7 + - - +
6843A ALA* 3.1 3.9 + - - +
6844A LYS* 2.8 34.0 + - - +
6995A VAL* 4.0 38.4 - - - +
6996A ASN* 4.6 17.5 - - - +
7107A FMT 2.9 23.1 + - - +
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Residues in contact with ASN6841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6839A MET* 3.2 3.3 - - + +
6840A MET* 1.3 77.9 - - - +
6842A VAL* 1.3 66.2 + - - +
6844A LYS* 3.4 32.5 + - - +
6845A TYR* 3.0 32.1 + - + +
6872A SER* 5.5 1.2 - - - -
6874A LYS* 6.0 3.6 - - - +
6878A PRO* 4.1 11.2 - - + +
6879A GLY* 4.8 0.5 - - - -
6928A ASP* 4.8 4.1 + - - +
7102A SAM 2.6 54.3 + - - +
7107A FMT 4.9 1.0 + - - -
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Residues in contact with VAL6842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6838A ILE* 3.9 14.4 - - + -
6839A MET* 3.0 19.1 + - + +
6841A ASN* 1.3 76.5 - - - +
6843A ALA* 1.3 56.9 + - - +
6846A THR* 2.8 42.7 + - - +
6878A PRO* 3.8 12.1 - - + -
6882A VAL* 3.7 23.4 - - + +
4295B VAL* 3.6 30.3 - - + -
4296B LYS 3.7 19.7 - - - +
4297B MET* 4.5 2.5 - - + -
4298B LEU* 4.4 15.5 - - + +
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Residues in contact with ALA6843 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6834A LEU* 3.7 21.1 - - + -
6838A ILE* 4.1 4.0 - - + +
6839A MET 3.1 8.1 + - - +
6840A MET 3.4 8.1 - - - +
6842A VAL* 1.3 76.9 - - - +
6844A LYS* 1.3 61.1 + - - +
6846A THR 3.3 0.7 + - - -
6847A GLN* 3.0 22.7 + - - +
6995A VAL* 4.0 9.6 - - + -
7042A LEU* 3.5 42.2 - - + +
4298B LEU* 4.4 3.8 - - - -
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Residues in contact with LYS6844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6840A MET* 2.8 24.8 + - - +
6841A ASN* 3.4 25.3 + - - +
6843A ALA* 1.3 70.9 - - - +
6845A TYR* 1.3 67.4 + - + +
6847A GLN 3.2 2.1 + - - -
6848A LEU* 3.0 24.4 + - - +
6928A ASP* 5.0 5.5 + - - +
6968A LYS* 4.3 6.3 - - - +
6993A THR* 3.6 24.3 - - + +
6995A VAL* 3.9 13.2 - - + +
6996A ASN* 3.7 18.1 - - - +
7001A GLU* 2.9 39.8 + - - +
7003A PHE* 4.1 16.8 - - + -
7102A SAM 5.9 2.0 - - - +
7104A FMT 4.4 4.9 + - - -
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Residues in contact with TYR6845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6841A ASN* 3.0 32.6 + - + +
6844A LYS* 1.3 82.3 - - + +
6846A THR* 1.3 62.2 + - - +
6848A LEU* 3.5 14.2 - - + +
6849A CYS* 2.9 34.4 + - - -
6867A HIS* 2.6 35.1 + + - -
6879A GLY* 3.4 31.4 - - - -
6882A VAL* 3.8 19.5 - - + -
6883A LEU* 4.2 14.8 - - + -
6926A ILE* 4.2 15.0 - - + +
6928A ASP* 3.0 22.6 - - + +
7003A PHE* 5.3 7.0 - + - -
7102A SAM 2.9 27.2 + - - -
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Residues in contact with THR6846 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6842A VAL* 2.8 26.4 + - - +
6843A ALA 3.6 4.7 - - - -
6844A LYS 3.2 0.2 - - - -
6845A TYR* 1.3 78.0 - - - +
6847A GLN* 1.3 57.6 + - - +
6850A GLN* 2.8 38.1 + - - +
6882A VAL* 3.7 18.7 - - - +
6885A GLN* 5.1 2.1 + - - -
7042A LEU* 4.1 7.6 - - + -
7045A MET* 3.7 32.3 - - + +
7048A PHE* 3.4 13.4 - - + -
4298B LEU* 3.8 21.6 + - + +
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Residues in contact with GLN6847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6804A GLN 4.5 0.4 + - - -
6805A PRO* 3.0 34.5 + - - +
6843A ALA 3.0 14.7 + - - +
6844A LYS 3.2 4.0 + - - +
6846A THR* 1.3 74.3 - - - +
6848A LEU* 1.3 65.4 + - - +
6850A GLN* 3.2 6.1 + - - +
6851A TYR* 3.0 21.1 + - - +
6991A PHE* 3.9 2.5 - - - -
6993A THR* 3.5 6.1 - - - -
6994A ASN* 3.2 5.8 + - - +
6995A VAL* 2.9 43.9 + - - +
7038A SER 3.3 21.2 + - - -
7039A SER* 4.2 4.8 - - - +
7041A SER* 3.1 27.5 + - - +
7042A LEU* 3.7 10.5 - - + +
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Residues in contact with LEU6848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6844A LYS 3.0 14.2 + - - +
6845A TYR* 3.2 19.7 + - + +
6847A GLN* 1.3 75.3 - - - +
6849A CYS* 1.3 60.0 + - - +
6851A TYR* 3.1 5.7 + - - +
6852A LEU* 2.8 45.6 + - + +
6883A LEU* 5.9 1.1 - - + -
6926A ILE* 4.7 13.0 - - + -
6966A ALA* 4.3 12.1 - - + -
6991A PHE* 4.0 14.8 - - + -
6993A THR* 4.2 5.5 - - + +
7003A PHE* 3.9 44.9 - - + -
7005A ILE* 4.0 26.2 - - + -
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Residues in contact with CYS6849 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6845A TYR* 2.9 20.3 + - - +
6848A LEU* 1.3 76.0 - - - +
6850A GLN* 1.3 65.9 + - - +
6852A LEU* 3.2 7.5 + - - +
6853A ASN* 3.0 28.4 + - - -
6882A VAL* 4.3 7.9 - - - -
6883A LEU* 3.8 19.3 - - - -
6886A TRP* 3.4 58.3 + - + -
7048A PHE* 3.7 11.2 - - + -
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Residues in contact with GLN6850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6805A PRO* 3.5 17.7 - - + +
6846A THR* 2.8 26.6 + - - +
6847A GLN* 3.2 12.0 + - - +
6849A CYS* 1.3 73.3 - - - +
6851A TYR* 1.3 62.4 + - - +
6853A ASN* 3.5 22.6 + - - +
6854A THR* 3.8 9.4 - - - +
7041A SER* 2.7 51.7 + - - -
7044A ASP 3.7 13.5 + - - -
7045A MET* 4.1 13.7 - - - +
7048A PHE* 3.8 16.5 - - + +
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Residues in contact with TYR6851 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6805A PRO* 3.9 10.3 - - + +
6806A GLY 5.7 0.9 - - - -
6808A ALA* 3.3 23.8 - - + +
6847A GLN 3.0 6.0 + - - +
6848A LEU 3.1 6.3 + - - +
6850A GLN* 1.3 73.7 - - - +
6852A LEU* 1.3 61.5 + - - +
6853A ASN 3.1 2.0 - - - -
6854A THR* 2.7 45.5 + - + -
6855A LEU* 3.9 21.9 - - + +
6987A TRP* 3.3 26.5 - - - -
6989A THR* 3.6 4.7 - - + +
6991A PHE* 3.3 50.9 - + + -
7005A ILE* 3.8 27.1 - - + -
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Residues in contact with LEU6852 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6848A LEU* 2.8 37.5 + - + +
6849A CYS* 3.2 3.8 + - - +
6851A TYR* 1.3 74.1 - - - +
6853A ASN* 1.3 63.1 + - - +
6855A LEU* 3.0 36.0 + - + +
6857A LEU* 4.0 21.8 - - + +
6883A LEU* 6.0 0.2 - - + -
6886A TRP* 3.6 38.8 - - + -
6924A LEU* 5.4 3.6 - - + -
6926A ILE* 4.5 17.3 - - + -
6965A VAL 5.5 0.7 - - - +
6966A ALA* 4.7 4.0 - - + -
7005A ILE* 3.9 35.7 - - + -
7050A LEU* 5.3 0.5 - - - +
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Residues in contact with ASN6853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6849A CYS 3.0 17.2 + - - -
6850A GLN* 3.5 17.3 - - - +
6851A TYR 3.1 0.4 - - - -
6852A LEU* 1.3 78.5 - - - +
6854A THR* 1.3 60.3 + - + +
6855A LEU 3.3 6.4 + - - +
6886A TRP* 2.8 20.4 + - - +
7047A LYS 3.6 13.7 + - - +
7048A PHE* 2.8 27.1 + - - +
7049A PRO 4.6 1.8 - - - -
7050A LEU* 3.6 24.9 - - - +
7051A LYS 5.7 0.2 - - - -
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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