Contacts of the helix formed by residues 796 - 813 (chain G) in PDB entry 1CDL
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 ALA 796 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C GLU* 5.0 10.3 - - + +
123C GLU* 2.7 39.4 + - + +
124C MET* 4.4 8.1 - - + +
127C GLU* 2.6 32.9 + - - +
41D GLN* 4.9 10.7 + - + +
87D GLU* 3.2 12.0 + - - -
797G ARG* 1.3 65.0 - - - +
798G ARG* 3.3 3.6 - - + -
799G LYS* 3.2 26.7 + - + +
800G TRP* 3.9 4.2 + - - -
814H SER* 5.5 9.6 - - - +
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Residues in contact with ARG 797 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C GLU* 2.9 18.6 + - - -
144C MET* 5.1 5.4 - - - -
87D GLU* 5.2 0.4 + - - -
796G ALA* 1.3 68.4 - - - +
798G ARG* 1.3 52.6 + - - +
800G TRP* 2.9 25.9 + - - +
801G GLN* 2.7 27.0 - - - +
814H SER* 5.8 1.8 - - - -
815H SER* 5.7 5.1 - - - -
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Residues in contact with ARG 798 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLU* 5.6 1.0 - - - +
10C ALA* 4.4 7.1 - - - +
11C GLU* 4.5 20.1 + - + +
14C GLU* 2.9 40.1 + - - +
47D GLU* 4.3 8.7 + - - +
50D ASP* 3.5 25.5 - - - +
51D MET* 4.2 16.3 - - - +
54D GLU* 3.6 24.5 + - - -
796G ALA* 4.9 1.3 - - + -
797G ARG* 1.3 74.2 - - - +
799G LYS* 1.3 62.4 + - - +
800G TRP 3.3 0.2 + - - -
801G GLN* 3.3 11.5 + - - +
802G LYS* 3.1 34.3 + - - +
814H SER* 2.8 54.0 + - - +
815H SER* 4.1 11.0 + - - +
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Residues in contact with LYS 799 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C MET* 3.4 17.5 - - + -
114C GLU* 3.9 26.8 + - - +
115C LYS 4.4 0.4 + - - -
116C LEU* 3.7 21.0 - - + +
120C GLU* 2.8 32.1 + - + +
124C MET* 4.0 13.2 - - - -
42D ASN 3.4 21.4 + - - -
43D PRO* 4.9 0.4 - - - +
47D GLU* 4.6 17.7 + - - +
796G ALA* 3.2 18.9 + - + +
798G ARG* 1.3 75.8 - - - +
800G TRP* 1.3 64.1 + - - +
802G LYS* 3.5 15.2 + - - +
803G THR* 3.1 31.2 + - - +
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Residues in contact with TRP 800 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C PHE* 4.5 7.2 - + - -
100C ILE* 5.2 0.9 - - + -
105C LEU* 4.0 36.3 - - + -
124C MET* 2.8 55.0 + - + +
125C ILE* 4.6 1.6 - - - -
127C GLU* 3.6 17.7 + - - -
128C ALA* 4.1 12.1 - - + -
136C VAL* 4.0 25.6 - - + -
141C PHE* 4.4 14.4 - + - -
144C MET* 3.6 32.5 - - + +
145C MET* 3.7 29.7 - - + +
796G ALA 4.2 0.7 - - - -
797G ARG 2.9 11.4 + - - +
799G LYS* 1.3 79.4 - - - +
801G GLN* 1.3 68.3 + - - +
803G THR* 2.9 10.1 + - - -
804G GLY* 2.8 26.0 + - - -
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Residues in contact with GLN 801 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLU* 3.8 25.7 - - - +
144C MET* 3.0 30.8 + - - +
145C MET* 5.1 9.0 - - - +
146C THR 6.5 0.9 - - - -
797G ARG* 2.7 35.1 + - - +
798G ARG* 3.3 9.6 + - - +
800G TRP* 1.3 77.5 - - - +
802G LYS* 1.3 66.6 + - - +
804G GLY* 4.7 2.0 - - - -
805G HIS* 2.8 42.3 + - + +
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Residues in contact with LYS 802 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLU* 4.7 5.8 - - - +
14C GLU* 3.0 58.6 + - + +
15C ALA* 4.0 2.6 - - - +
18C LEU* 4.3 13.2 - - + -
114C GLU* 3.9 14.8 - - + +
47D GLU* 2.9 34.9 + - + -
798G ARG* 3.1 21.6 + - - +
799G LYS* 3.5 26.0 - - - +
800G TRP 3.2 0.2 - - - -
801G GLN* 1.3 80.4 - - - +
803G THR* 1.3 64.2 + - - +
805G HIS* 3.1 14.1 + - - +
806G ALA* 3.2 12.1 + - - +
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Residues in contact with THR 803 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 4.6 0.2 - - - -
92C PHE* 3.9 18.7 - - - -
105C LEU* 5.2 1.2 - - - +
109C MET* 3.2 23.7 - - + +
112C LEU* 4.1 10.7 - - - +
114C GLU* 3.1 35.7 - - - +
124C MET* 5.2 0.2 - - - +
799G LYS 3.1 14.9 + - - +
800G TRP* 2.9 17.0 + - - -
802G LYS* 1.3 74.5 - - - +
804G GLY* 1.3 60.1 + - - +
806G ALA* 3.3 5.4 + - - +
807G VAL* 2.9 33.2 + - - +
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Residues in contact with GLY 804 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ALA* 5.4 0.8 - - - +
92C PHE* 4.8 4.0 - - - -
141C PHE* 5.8 0.2 - - - -
145C MET* 3.6 24.2 - - - -
800G TRP 2.8 17.9 + - - -
801G GLN 3.8 0.9 - - - -
803G THR* 1.3 78.2 + - - +
805G HIS* 1.3 51.4 + - - +
807G VAL* 3.2 8.0 + - - +
808G ARG* 2.8 42.4 + - - +
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Residues in contact with HIS 805 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLN* 5.1 2.8 + - - +
11C GLU* 4.0 32.4 + - + +
12C PHE* 3.3 32.6 - + + -
15C ALA* 3.7 14.6 - - + -
68C PHE* 5.0 1.5 - - + -
72C MET* 3.8 5.6 - - + +
801G GLN* 2.8 47.3 + - + +
802G LYS 3.6 3.8 - - - +
804G GLY* 1.3 71.6 - - - +
806G ALA* 1.3 53.5 + - - +
808G ARG* 3.0 38.0 + - - +
809G ALA* 2.8 34.8 + - - +
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Residues in contact with ALA 806 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ALA* 4.2 3.7 - - + +
18C LEU* 3.7 26.9 - - + -
19C PHE* 3.1 43.8 - - + -
112C LEU* 4.2 14.5 - - + +
802G LYS 3.2 3.1 + - - +
803G THR 3.4 8.7 - - - +
805G HIS* 1.3 80.5 - - - +
807G VAL* 1.3 63.3 + - - +
809G ALA* 3.3 6.8 - - - +
810G ILE* 3.5 8.1 + - - +
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Residues in contact with VAL 807 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 5.6 2.5 - - + -
88C ALA* 3.9 31.8 - - + +
91C VAL* 4.1 20.0 - - + -
92C PHE* 3.6 30.3 - - + -
108C VAL* 4.5 8.1 - - + -
112C LEU* 4.2 15.0 - - + -
803G THR 2.9 22.0 + - - +
804G GLY* 3.6 4.5 - - - +
806G ALA* 1.3 76.8 - - - +
808G ARG* 1.3 61.8 + - - +
810G ILE* 3.2 27.0 + - + +
811G GLY* 3.6 3.6 + - - -
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Residues in contact with ARG 808 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PHE* 4.3 5.7 - - - -
72C MET* 3.8 14.8 + - + +
84C GLU* 3.1 35.5 + - + +
85C ILE* 4.6 15.5 - - + -
88C ALA* 4.4 17.7 - - + -
145C MET* 5.6 14.6 + - + +
804G GLY 2.8 23.5 + - - +
805G HIS* 3.0 38.4 + - - +
807G VAL* 1.3 70.8 - - - +
809G ALA* 1.3 65.7 + - - +
810G ILE 3.2 0.2 + - - -
811G GLY* 3.2 3.9 + - - +
812G ARG* 2.8 57.6 + - - +
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Residues in contact with ALA 809 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 3.4 19.7 - - + -
68C PHE* 3.9 22.2 - - + -
71C MET* 4.1 4.7 - - + +
72C MET* 4.0 13.0 - - - +
805G HIS 2.8 13.6 + - - +
806G ALA 3.3 12.1 - - - +
807G VAL 3.2 0.4 - - - -
808G ARG* 1.3 76.0 - - - +
810G ILE* 1.3 63.2 + - - +
812G ARG* 3.2 3.3 + - - +
813G LEU* 2.9 29.8 + - + +
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Residues in contact with ILE 810 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 4.7 10.1 - - + -
32C LEU* 5.3 1.1 - - + -
35C VAL* 4.4 7.4 - - + -
36C MET* 3.5 41.5 - - + -
39C LEU* 3.7 32.1 - - + -
41C GLN* 3.7 27.1 - - - +
51C MET* 4.5 0.3 - - - +
91C VAL* 5.9 1.6 - - + -
806G ALA 3.5 12.3 + - - +
807G VAL* 3.2 17.2 + - + +
808G ARG 3.2 0.4 - - - -
809G ALA* 1.3 75.7 - - - +
811G GLY* 1.3 67.3 + - - +
813G LEU* 2.8 26.3 + - - +
814G SER* 3.4 10.6 + - - +
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Residues in contact with GLY 811 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C GLU* 5.6 6.3 - - - -
87C GLU* 3.9 27.2 - - - +
807G VAL 3.6 4.4 + - - -
808G ARG* 3.2 7.4 + - - -
810G ILE* 1.3 80.3 - - - +
812G ARG* 1.3 59.8 + - - +
814G SER* 3.3 23.4 + - - +
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Residues in contact with ARG 812 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLU* 2.9 20.5 - - - +
71C MET* 3.2 36.1 + - + -
72C MET* 3.8 29.6 + - - +
74C ARG* 2.5 30.5 + - - +
75C LYS* 4.6 2.4 - - - +
76C MET* 4.1 27.0 - - - +
81C SER* 5.7 0.8 + - - -
84C GLU* 2.7 36.2 + - - +
808G ARG* 2.8 41.8 + - - +
809G ALA* 3.6 4.5 - - - +
811G GLY* 1.3 70.9 - - - +
813G LEU* 1.3 54.3 + - - +
814G SER* 2.7 19.4 + - - +
815G SER* 4.8 1.0 - - - -
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Residues in contact with LEU 813 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 4.9 4.7 - - + -
32C LEU* 3.9 29.6 - - + -
51C MET* 3.1 61.9 - - + +
54C GLU* 3.1 12.6 - - - +
55C VAL* 3.8 8.7 - - + -
63C ILE* 3.9 20.6 - - + -
68C PHE* 5.6 1.3 - - + -
71C MET* 3.6 30.5 - - + -
809G ALA* 2.9 23.1 + - + +
810G ILE* 2.8 10.1 + - - +
812G ARG* 1.3 73.1 - - - +
814G SER* 1.3 58.1 + - - +
815G SER 4.1 0.3 + - - -
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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