Contacts of the helix formed by residues 874 - 889 (chain D) in PDB entry 6MZL
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 LEU 874 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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873D LEU* 1.3 75.3 - - - +
875D GLN* 1.3 65.0 + - - +
876D ALA 3.5 0.9 - - - -
877D PRO* 3.8 19.1 - - + -
878D LEU* 3.3 25.1 + - - +
56Q GLN* 3.4 24.5 - - + +
57Q VAL 2.6 24.9 + - - +
58Q LEU* 4.1 6.3 - - - +
59Q THR* 4.4 22.2 - - + -
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Residues in contact with GLN 875 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871D THR* 4.1 25.2 - - + +
873D LEU 3.4 6.3 + - - +
874D LEU* 1.3 73.4 - - - +
876D ALA* 1.3 59.3 + - - +
878D LEU* 4.3 1.5 - - - +
879D GLN* 2.8 54.4 + - + +
896D PRO* 4.3 27.3 + - - +
899D VAL* 5.8 6.1 - - + +
900D SER* 5.3 11.6 - - - +
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Residues in contact with ALA 876 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875D GLN* 1.3 79.2 - - - +
877D PRO* 1.4 64.9 - - + +
879D GLN* 3.4 7.3 + - - +
880D ARG* 2.9 49.6 + - - +
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Residues in contact with PRO 877 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874D LEU* 3.8 30.1 - - + +
876D ALA* 1.4 93.6 - - + +
878D LEU* 1.3 58.2 + - - +
880D ARG* 3.4 27.5 + - - +
881D ARG* 3.0 34.7 + - - +
55Q ASN 4.9 12.3 - - - +
56Q GLN 4.0 14.6 - - - +
57Q VAL* 4.1 8.5 - - + -
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Residues in contact with LEU 878 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873D LEU* 3.7 31.4 - - + -
874D LEU 3.3 16.1 + - - +
875D GLN* 4.3 1.1 - - - +
876D ALA 3.4 0.2 - - - -
877D PRO* 1.3 82.3 - - - +
879D GLN* 1.3 57.7 + - - +
881D ARG* 3.2 15.6 + - + +
882D ILE* 2.8 53.8 + - + +
899D VAL* 5.6 4.0 - - + +
902D VAL* 5.5 3.4 - - + -
903D SER* 5.0 9.0 - - - +
57Q VAL* 3.7 25.9 - - + +
92Q ILE* 3.7 27.8 - - + -
96Q VAL* 5.5 1.1 - - + -
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Residues in contact with GLN 879 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875D GLN* 2.8 45.2 + - + +
876D ALA* 3.7 6.6 - - - +
878D LEU* 1.3 76.2 - - - +
880D ARG* 1.3 58.6 + - + +
882D ILE* 3.4 9.5 + - - +
883D LEU* 2.9 40.3 + - + +
894D LEU* 3.4 38.3 - - + +
896D PRO* 5.4 4.8 - - - +
899D VAL* 4.8 10.3 - - + +
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Residues in contact with ARG 880 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876D ALA* 2.9 42.5 + - - +
877D PRO* 3.4 30.3 - - - +
878D LEU 3.3 0.2 - - - -
879D GLN* 1.3 78.7 - - + +
881D ARG* 1.3 58.5 + - + +
883D LEU* 3.8 9.1 - - + +
884D GLU* 2.9 30.5 + - - +
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Residues in contact with ARG 881 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877D PRO* 3.0 23.1 + - - +
878D LEU* 3.2 12.7 + - + +
880D ARG* 1.3 74.8 - - + +
882D ILE* 1.3 62.1 + - + +
884D GLU* 3.5 15.1 - - - +
885D ILE* 2.9 45.1 + - + +
55Q ASN 4.4 14.8 + - - -
57Q VAL* 4.5 21.2 - - - +
89Q ASP* 6.1 2.4 - - - +
93Q GLU* 3.9 20.8 + - - +
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Residues in contact with ILE 882 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878D LEU* 2.8 40.5 + - + +
879D GLN* 3.8 4.9 - - - +
880D ARG 3.3 0.2 - - - -
881D ARG* 1.3 75.2 - - - +
883D LEU* 1.3 58.7 + - + +
885D ILE* 3.5 1.2 + - - +
886D GLY* 2.9 26.9 + - - -
894D LEU* 4.3 17.3 - - + -
899D VAL* 3.7 29.4 - - + -
902D VAL* 4.8 11.7 - - + -
96Q VAL* 3.7 36.1 - - + -
99Q ALA* 6.5 1.1 - - + -
100Q CYS* 5.0 4.3 - - - -
111Q LEU* 6.0 6.7 - - + -
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Residues in contact with LEU 883 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879D GLN* 2.9 32.6 + - + +
880D ARG* 3.8 8.3 - - + +
882D ILE* 1.3 75.6 - - + +
884D GLU* 1.3 56.2 + - - +
886D GLY* 5.0 0.7 - - - -
887D LYS* 2.9 47.2 + - - +
891D ILE* 4.2 2.0 - - + +
892D THR 3.3 26.0 - - - +
893D GLU* 4.0 13.9 - - - +
894D LEU* 3.7 26.0 - - + -
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Residues in contact with GLU 884 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880D ARG 2.9 17.4 + - - +
881D ARG* 3.5 19.5 + - - +
882D ILE 3.3 0.2 - - - -
883D LEU* 1.3 76.3 - - - +
885D ILE* 1.3 62.6 + - + +
887D LYS* 3.2 7.0 + - - +
888D LYS* 3.0 55.0 + - + +
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Residues in contact with ILE 885 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881D ARG* 2.9 28.0 + - + +
882D ILE 4.2 0.2 - - - +
884D GLU* 1.3 81.4 - - + +
886D GLY* 1.3 60.0 + - - +
888D LYS* 3.5 7.4 + - + +
889D HIS* 2.9 46.6 + - + +
93Q GLU* 3.4 35.9 - - - +
96Q VAL* 3.9 27.4 - - + -
97Q THR* 5.8 3.1 - - - +
100Q CYS* 4.1 7.8 - - - -
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Residues in contact with GLY 886 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882D ILE 2.9 17.8 + - - -
883D LEU* 3.8 0.7 - - - -
885D ILE* 1.3 75.4 - - - +
887D LYS* 1.3 51.2 + - - +
889D HIS* 3.0 3.2 + - - -
890D GLY 2.6 16.8 + - - -
891D ILE* 2.4 49.2 + - - -
100Q CYS* 4.0 12.7 - - - -
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Residues in contact with LYS 887 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883D LEU* 2.9 33.2 + - - +
884D GLU* 3.9 5.2 - - - +
886D GLY* 1.3 74.7 - - - +
888D LYS* 1.3 66.5 + - - +
890D GLY* 3.7 7.4 + - - -
891D ILE 3.5 13.2 - - - +
892D THR* 3.4 41.6 + - - +
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Residues in contact with LYS 888 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884D GLU* 3.0 45.3 + - + +
885D ILE* 3.8 9.4 - - - +
886D GLY 3.2 0.4 - - - -
887D LYS* 1.3 80.6 - - - +
889D HIS* 1.3 72.0 + - + +
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Residues in contact with HIS 889 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885D ILE* 2.9 39.1 + - + +
886D GLY 3.0 5.5 + - - +
888D LYS* 1.3 86.5 - - + +
890D GLY* 1.3 58.3 + - - +
891D ILE* 3.7 5.7 - - + +
100Q CYS* 4.8 17.6 - - + +
104Q ARG* 4.6 24.1 + - + +
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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
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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