Contacts of the helix formed by residues 9 - 27 (chain P) in PDB entry 1L0V
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 ASP 9 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710D CE1 4.5 25.6 - - - +
810D CE1 3.8 21.8 - - - +
198N GLN* 4.4 8.1 + - - +
235N PHE* 4.3 6.3 - - - -
7P ARG 5.0 0.5 - - - +
8P SER* 1.3 82.7 + - - +
10P GLU* 0.8 79.3 + - - +
11P PRO* 2.6 5.4 - - - +
12P VAL* 2.9 19.6 + - - +
13P PHE* 4.1 12.6 + - + -
97P LYS* 3.0 37.5 + - - -
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Residues in contact with GLU 10 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198N GLN* 4.5 10.4 - - - +
202N TRP* 3.5 40.0 - - + +
8P SER* 3.8 9.6 - - - +
9P ASP* 0.8 95.4 - - - +
11P PRO* 1.3 58.4 - - + +
12P VAL 2.8 2.0 + - - -
13P PHE* 3.1 11.0 + - - +
14P TRP* 2.7 39.4 + - + +
80P HIS* 3.1 30.8 - - + -
84P HIS* 3.4 20.9 + - - -
97P LYS* 5.3 4.9 - - - -
101P TYR* 4.2 2.8 + - - -
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Residues in contact with PRO 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202N TRP* 3.2 39.7 - - + +
231N SER* 4.1 4.0 - - - +
232N SER* 3.8 17.9 + - - +
235N PHE* 3.8 36.1 - - + -
8P SER 3.8 6.7 - - - +
9P ASP* 2.6 8.7 - - - +
10P GLU* 1.3 94.1 - - + +
12P VAL* 1.3 59.0 + - - +
14P TRP* 4.1 1.1 - - + -
15P GLY* 3.4 16.1 + - - -
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Residues in contact with VAL 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D TRP* 4.1 30.7 - - + -
710D CE1 4.5 26.5 - - - +
235N PHE* 4.2 27.4 - - + -
9P ASP 3.7 10.3 - - - +
10P GLU 2.8 2.6 + - - -
11P PRO* 1.3 79.6 - - - +
13P PHE* 1.3 73.8 + - + +
14P TRP 3.2 0.2 - - - -
15P GLY* 3.2 9.4 + - - -
16P LEU* 3.2 21.6 + - + +
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Residues in contact with PHE 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710D CE1 4.1 28.7 - - - -
810D CE1 4.0 23.8 - - + -
9P ASP* 4.4 18.2 - - + -
10P GLU* 3.1 9.9 + - - +
12P VAL* 1.3 79.2 - - + +
14P TRP* 1.3 67.8 + - - +
16P LEU* 3.1 15.7 + - + +
17P PHE* 2.8 26.5 + - - +
76P TRP* 5.1 2.7 - + - -
80P HIS* 3.7 14.6 + - + +
97P LYS* 3.9 18.2 - - + -
101P TYR* 3.3 68.0 - + + +
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Residues in contact with TRP 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202N TRP* 3.4 20.6 - + + -
225N GLN* 4.6 7.2 - - - -
228N LYS* 3.4 31.3 - - + +
229N VAL* 3.9 24.9 - - + -
232N SER* 3.5 29.8 - - - -
801N MQ7 2.9 84.7 + + + +
10P GLU* 2.7 21.5 + - + +
11P PRO* 4.1 1.8 - - + -
13P PHE* 1.3 76.5 - - - +
15P GLY* 1.3 64.0 + - - +
17P PHE* 3.3 14.1 + + - -
18P GLY* 2.8 28.4 + - - -
80P HIS* 4.2 7.2 - - - +
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Residues in contact with GLY 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801N MQ7 5.2 5.3 - - - +
11P PRO 3.4 11.3 + - - -
12P VAL 3.2 8.9 + - - -
13P PHE 3.1 0.8 - - - -
14P TRP* 1.3 90.6 - - - +
16P LEU* 1.3 60.1 + - - +
18P GLY* 3.7 1.1 + - - -
19P ALA* 3.4 18.4 + - - +
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Residues in contact with LEU 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710D CE1 4.4 36.6 - - - +
12P VAL* 3.2 19.4 + - + +
13P PHE* 3.1 16.9 + - + +
15P GLY* 1.3 73.1 - - - +
17P PHE* 1.3 56.9 + - - +
18P GLY 3.0 1.3 - - - -
19P ALA* 2.9 9.3 + - + +
20P GLY* 2.7 32.9 + - - -
73P LEU* 5.5 3.5 - - + +
76P TRP* 4.0 45.9 - - + +
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Residues in contact with PHE 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801N MQ7 3.6 52.5 - + + -
86O TRP* 3.6 32.3 - + - -
13P PHE 2.8 16.0 + - - +
14P TRP* 3.6 14.4 - + - -
16P LEU* 1.3 76.5 - - - +
18P GLY* 1.3 60.6 + - - +
21P GLY* 2.8 26.7 + - - -
76P TRP 4.2 2.1 + - - -
77P CYS* 3.7 29.8 - - - +
80P HIS* 3.4 35.4 - + + -
81P ARG* 3.6 28.0 - - + -
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Residues in contact with GLY 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801N MQ7 3.7 29.0 - - - +
86O TRP* 3.5 12.2 - - - -
14P TRP 2.8 16.6 + - - -
15P GLY 4.1 1.1 - - - -
16P LEU 2.9 0.6 + - - -
17P PHE* 1.3 79.5 - - - +
19P ALA* 1.3 65.4 + - - +
22P MET* 3.2 21.8 + - - +
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Residues in contact with ALA 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801N MQ7 4.8 1.0 - - - +
15P GLY 3.4 12.4 + - - +
16P LEU* 2.9 9.7 + - + +
18P GLY* 1.3 74.0 - - - +
20P GLY* 1.3 62.9 + - - +
22P MET* 3.3 7.2 + - - +
23P TRP* 3.0 24.5 + - - +
73P LEU* 4.7 15.5 - - + +
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Residues in contact with GLY 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P LEU 2.7 15.2 + - - -
17P PHE 3.6 1.6 - - - -
19P ALA* 1.3 77.9 - - - +
21P GLY* 1.3 57.3 + - - +
23P TRP* 3.1 4.7 + - - +
24P SER* 2.9 29.8 + - - -
73P LEU* 3.4 34.5 - - - +
76P TRP* 5.8 0.2 - - - -
77P CYS* 3.7 8.7 - - - -
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Residues in contact with GLY 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82O HIS* 2.9 25.8 + - - -
86O TRP* 3.6 20.8 - - - -
17P PHE 2.8 20.3 + - - -
20P GLY* 1.3 72.4 - - - +
22P MET* 1.3 56.9 + - - +
24P SER* 3.5 7.0 - - - -
25P ALA* 3.0 17.0 + - - +
77P CYS* 3.5 10.7 - - - +
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Residues in contact with MET 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801N MQ7 5.3 11.7 - - + -
86O TRP* 2.9 41.1 - - + +
87O PHE* 4.6 5.8 - - - -
90O ALA* 4.5 13.5 - - + -
112O LEU* 4.8 13.0 - - + -
18P GLY 3.2 12.6 + - - +
19P ALA* 3.5 11.0 - - - +
20P GLY 3.1 0.2 - - - -
21P GLY* 1.3 75.1 - - - +
23P TRP* 1.3 64.4 + - - +
25P ALA* 2.9 5.8 + - - +
26P ILE* 2.8 46.4 - - + +
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Residues in contact with TRP 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19P ALA 3.0 13.6 + - - +
20P GLY 3.7 6.1 - - - +
22P MET* 1.3 76.1 - - - +
24P SER* 1.3 65.2 + - - +
25P ALA 3.1 0.3 + - - -
26P ILE* 5.0 0.4 - - - -
27P ILE* 3.0 58.5 + - + +
66P PHE* 3.7 37.7 - + - -
69P LEU* 4.0 24.5 - - + -
70P MET* 3.2 44.3 - - + +
73P LEU* 3.8 25.1 - - + -
74P PRO* 4.2 18.8 - - + -
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Residues in contact with SER 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O ALA* 6.0 4.9 - - - -
79O ALA* 5.0 1.6 - - - +
82O HIS* 3.3 27.9 + - - -
83O THR* 3.8 3.5 + - - -
20P GLY 2.9 17.8 + - - -
21P GLY* 3.5 3.3 - - - -
23P TRP* 1.3 80.3 - - - +
25P ALA* 1.3 59.9 + - - +
28P ALA* 2.8 37.2 - - - +
74P PRO* 4.3 22.6 - - - +
77P CYS* 4.4 5.9 - - - +
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Residues in contact with ALA 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82O HIS* 3.9 7.6 - - + +
83O THR* 2.8 36.3 + - - +
86O TRP* 3.9 13.7 - - + -
87O PHE* 3.8 22.4 - - + -
116O THR* 3.8 1.9 + - - -
21P GLY 3.0 18.3 + - - +
22P MET 2.9 10.6 + - - +
24P SER* 1.3 80.5 - - - +
26P ILE* 1.3 61.7 + - + +
29P PRO* 3.7 5.5 - - - +
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Residues in contact with ILE 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87O PHE* 3.9 10.8 - - + -
112O LEU* 5.8 2.2 - - + -
115O VAL* 4.3 20.9 - - + -
116O THR* 3.6 27.7 - - - +
119O ALA* 3.9 26.3 - - + +
120O THR* 4.4 4.9 + - - -
22P MET* 2.8 49.9 + - + +
23P TRP* 5.1 0.2 - - - -
25P ALA* 1.3 85.4 - - + +
27P ILE* 1.3 80.6 + - + +
29P PRO* 3.8 10.0 - - - +
30P VAL* 4.9 1.4 - - - +
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Residues in contact with ILE 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119O ALA* 5.3 2.7 - - + -
123O ILE* 4.1 23.8 - - + -
23P TRP* 3.0 60.0 + - + +
26P ILE* 1.3 92.6 - - + +
28P ALA* 1.3 66.6 + - - +
29P PRO 3.6 0.2 - - - -
30P VAL* 3.0 20.7 - - - +
31P MET* 3.4 11.3 + - + +
66P PHE* 4.1 5.2 - - + -
70P MET* 3.5 24.2 - - - -
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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
------------------------------------------------------------
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