Contacts of the helix formed by residues 1000 - 1005 (chain M) in PDB entry 5D4D
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 MET1000 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569M VAL* 4.3 5.4 - - + -
704M HIS* 3.5 32.8 - - + +
831M ARG* 3.3 35.9 - - - +
836M GLY 4.8 0.2 - - - -
837M ASP* 3.6 14.6 - - + +
996M LYS* 3.9 27.1 - - + -
997M LEU 3.9 7.4 - - - +
998M TYR* 3.3 34.0 + - + +
999M HIS* 1.3 78.6 - - - +
1001M VAL* 1.3 65.9 + - - +
1002M GLU* 4.3 5.8 - - + +
1003M ASP* 3.0 26.0 + - - +
1004M LYS* 3.5 16.5 + - - +
630N VAL* 5.2 0.7 - - - -
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Residues in contact with VAL1001 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834M GLN* 3.7 15.7 - - - +
835M VAL 3.3 21.1 - - - +
836M GLY 3.7 18.0 + - - +
837M ASP* 3.2 16.4 + - - +
1000M MET* 1.3 70.2 - - - +
1002M GLU* 1.3 65.4 + - - +
1004M LYS 3.1 0.6 + - - +
1005M MET* 3.0 25.5 + - - +
629N SER* 3.8 9.6 - - - +
630N VAL* 4.0 15.9 - - + +
724N GLN* 3.6 28.7 - - + +
725N SER* 3.3 20.2 - - - +
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Residues in contact with GLU1002 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795M GLY* 4.2 18.0 - - - +
796M GLU* 5.9 0.3 - - - -
829M GLN* 3.0 30.0 + - - +
831M ARG* 3.2 40.7 + - - +
834M GLN* 3.3 21.9 + - - +
1000M MET* 3.1 4.9 - - + -
1001M VAL* 1.3 81.8 - - - +
1003M ASP* 1.3 60.2 + - - +
1005M MET* 4.3 3.1 + - - +
1024M LYS* 4.0 7.8 + - - -
724N GLN* 3.8 27.8 + - - +
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Residues in contact with ASP1003 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796M GLU* 6.1 1.2 - - - +
831M ARG* 2.7 44.8 + - - -
998M TYR* 4.8 9.3 - - - +
1000M MET* 3.0 23.7 + - - +
1002M GLU* 1.3 79.9 - - - +
1004M LYS* 1.3 63.1 + - + +
1005M MET 3.5 0.2 - - - -
1024M LYS* 2.8 29.8 + - - +
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Residues in contact with LYS1004 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999M HIS* 2.9 52.8 + - + +
1000M MET 3.6 11.9 - - - +
1001M VAL 3.1 5.5 + - - +
1003M ASP* 1.3 82.8 - - + +
1005M MET* 1.3 63.1 + - - +
1006M HIS* 3.3 7.2 + - - +
1024M LYS* 5.0 2.1 - - - +
628N ARG* 3.7 13.7 - - - +
629N SER* 4.3 4.3 - - - -
630N VAL* 4.4 15.7 - - + -
742N GLY 5.6 1.2 + - - -
744N GLN* 3.4 38.7 + - - +
101R A 4.6 9.7 + - - -
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Residues in contact with MET1005 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795M GLY* 6.0 6.0 - - - -
1001M VAL 3.0 16.4 + - - +
1002M GLU 4.3 2.4 + - - +
1003M ASP 3.5 1.0 - - - -
1004M LYS* 1.3 77.6 - - - +
1006M HIS* 1.3 67.7 + - - +
1007M ALA 5.4 0.4 - - - +
1024M LYS* 3.5 18.2 + - - -
628N ARG 3.8 3.4 - - - -
629N SER* 3.6 11.4 + - - +
645N PRO* 4.3 4.9 - - - -
647N ARG* 3.9 26.2 - - + -
648N MET* 3.6 33.9 - - + +
724N GLN* 3.4 54.7 - - - +
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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
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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