Contacts of the helix formed by residues 1000 - 1005 (chain C) in PDB entry 6KQG
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569C VAL* 4.3 2.5 - - + -
702C SER* 4.7 0.2 - - - -
704C HIS* 3.4 24.5 - - + -
831C ARG* 3.2 46.7 - - - +
836C GLY 4.9 0.2 - - - -
837C ASP* 3.8 22.9 - - + +
996C LYS* 3.9 24.2 - - + -
997C LEU 3.9 9.2 - - - +
998C TYR* 3.2 35.9 + - + +
999C HIS* 1.3 76.2 - - - +
1001C VAL* 1.3 63.6 + - - +
1002C GLU* 3.0 9.5 + - + +
1003C ASP* 3.0 18.8 + - - +
1004C LYS* 3.5 14.3 - - - +
630D VAL* 5.4 0.2 - - - -
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Residues in contact with VAL1001 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834C GLN* 3.3 23.3 - - - +
835C VAL 3.6 17.9 - - - +
836C GLY* 4.0 16.4 + - - +
837C ASP* 3.4 10.8 + - - +
1000C MET* 1.3 72.5 - - - +
1002C GLU* 1.3 63.6 + - - +
1003C ASP 3.3 0.2 - - - -
1004C LYS 3.7 2.0 - - - +
1005C MET* 3.0 25.9 + - - +
629D SER* 3.6 9.9 - - - +
630D VAL* 4.1 18.6 - - + +
724D GLN* 3.3 34.9 + - + +
725D SER* 3.6 12.3 - - - +
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Residues in contact with GLU1002 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795C GLY* 4.5 20.9 - - - +
829C GLN* 3.9 18.7 + - - +
831C ARG* 3.1 48.2 + - - +
834C GLN* 4.0 13.5 + - - +
1000C MET* 4.3 3.9 - - + +
1001C VAL* 1.3 84.2 - - - +
1003C ASP* 1.3 62.2 + - - +
1005C MET 4.0 5.7 + - - +
1024C LYS* 4.2 8.3 + - - -
724D GLN* 3.8 25.3 + - - +
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Residues in contact with ASP1003 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831C ARG* 2.9 41.8 + - - -
998C TYR* 4.0 19.2 - - - +
1000C MET* 3.0 20.8 + - - +
1002C GLU* 1.3 76.6 - - - +
1004C LYS* 1.3 63.9 + - + +
1005C MET 3.7 0.2 - - - -
1024C LYS* 3.2 34.2 + - - +
18G A 5.4 4.5 - - - +
19G G 5.6 0.2 + - - -
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Residues in contact with LYS1004 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998C TYR 5.5 0.2 - - - -
999C HIS* 3.0 52.7 + - + +
1000C MET 3.5 12.1 - - - +
1001C VAL* 3.2 6.0 + - + +
1003C ASP* 1.3 85.6 - - + +
1005C MET* 1.3 63.6 + - - +
1006C HIS* 3.3 8.3 + - - +
1024C LYS* 5.0 1.2 - - - +
628D ARG* 3.5 17.8 - - - +
629D SER* 4.3 1.7 - - - -
630D VAL* 4.1 19.7 - - + +
742D GLY 5.4 3.2 + - - +
744D GLN* 3.1 37.9 + - - +
18G A 5.7 12.8 - - - +
6I G 4.3 11.1 + - - -
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Residues in contact with MET1005 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795C GLY* 5.9 6.9 - - - -
1001C VAL 3.0 15.1 + - - +
1002C GLU 4.0 2.9 + - - +
1003C ASP 3.7 0.6 - - - -
1004C LYS* 1.3 76.6 - - - +
1006C HIS* 1.3 64.6 + - - +
1007C ALA* 5.9 0.4 - - + +
1024C LYS* 4.0 13.0 - - - -
628D ARG 3.7 0.9 - - - -
629D SER* 3.5 23.8 + - - +
645D PRO* 4.3 5.6 - - - -
647D ARG* 4.2 28.0 - - + +
648D MET* 3.6 30.7 - - + +
724D GLN* 3.4 46.7 - - - +
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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