Contacts of the helix formed by residues 18 - 34 (chain L) in PDB entry 6XAV
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 PHE 18 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L ALA* 4.6 10.8 - - + -
15L PHE* 3.8 18.5 + + + +
17L GLY* 1.3 75.5 - - - +
19L GLU* 1.3 61.7 + - - +
20L GLY 3.2 2.7 - - - +
21L ARG* 3.6 31.4 - - + -
22L VAL* 3.2 36.5 + - + +
67L GLY* 4.4 3.4 + - - -
87L PRO 4.6 0.9 - - - -
88L ARG* 3.3 51.4 - - + -
7N C 3.1 33.0 - - + +
8N C 3.1 24.9 - - - -
27T C 4.7 3.6 - - - -
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Residues in contact with GLU 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLU* 3.3 23.8 - - + +
17L GLY 3.3 4.7 + - - +
18L PHE* 1.3 77.7 - - - +
20L GLY* 1.3 68.3 + - - +
22L VAL* 3.5 11.3 - - - +
23L ALA 3.8 1.2 + - - -
43L MET 4.6 0.9 - - - +
44L VAL* 3.6 14.7 - - - +
45L PRO* 3.4 29.3 - - - +
63L LYS* 3.5 29.1 + - - +
65L PHE 3.4 19.8 - - - +
66L PRO* 5.0 0.2 - - - +
67L GLY* 3.7 20.7 + - - +
68L TYR 4.7 2.8 - - - +
69L VAL* 3.6 20.3 - - + +
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Residues in contact with GLY 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLU* 3.0 38.8 - - - +
107B GLY* 4.2 7.2 - - - -
17L GLY 4.7 2.0 + - - -
18L PHE* 3.2 2.0 - - - +
19L GLU* 1.3 82.1 - - - +
21L ARG* 1.3 61.0 + - - +
22L VAL 3.5 0.2 + - - -
23L ALA 3.6 5.0 + - - -
24L THR* 3.8 6.9 - - - +
63L LYS* 5.9 1.7 - - - +
7N C 5.0 5.0 + - - -
28T C 4.0 6.1 - - - -
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Residues in contact with ARG 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478I ARG* 4.0 23.8 - - - +
18L PHE* 3.6 26.2 + - + -
20L GLY* 1.3 69.8 - - - +
22L VAL* 1.3 64.6 + - - +
23L ALA 3.1 2.7 - - - -
24L THR* 2.7 30.4 + - - +
25L SER* 3.3 12.0 + - - +
88L ARG* 3.2 38.9 + - - +
7N C 4.9 2.4 + - - +
27T C 3.3 30.3 + - - +
28T C 3.3 34.3 + - - +
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Residues in contact with VAL 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L VAL* 5.1 9.9 - - + +
14L ALA* 5.6 1.1 - - + -
18L PHE* 3.2 35.4 + - + +
19L GLU* 3.5 12.1 - - - +
21L ARG* 1.3 78.9 - - - +
23L ALA* 1.3 61.7 + - + +
25L SER* 4.0 4.3 + - - -
26L LEU* 3.2 27.3 + - + +
69L VAL* 4.3 13.9 - - + -
86L VAL* 4.3 16.7 - - + +
88L ARG* 4.0 12.1 - - - +
89L VAL* 3.9 30.3 - - + -
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Residues in contact with ALA 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLU* 3.4 45.1 - - + +
19L GLU 4.0 2.9 - - - +
20L GLY 3.6 1.0 + - - +
21L ARG 3.1 0.8 - - - -
22L VAL* 1.3 82.6 - - + +
24L THR* 1.3 60.3 + - - +
25L SER 3.2 0.4 - - - -
26L LEU* 3.5 7.7 - - + +
27L ARG* 2.9 38.0 + - - +
42L VAL* 4.9 10.3 - - + -
69L VAL* 5.1 4.9 - - + -
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Residues in contact with THR 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LYS* 3.9 41.0 - - + +
106B GLU 4.2 5.6 - - - +
108B GLU* 4.6 8.3 - - + +
20L GLY 3.8 13.0 - - - +
21L ARG* 2.7 33.6 + - - +
23L ALA* 1.3 76.9 - - - +
25L SER* 1.3 60.5 + - - +
27L ARG* 3.9 3.3 + - - +
28L GLU* 3.3 28.1 + - - +
28T C 5.7 2.9 - - - +
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Residues in contact with SER 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477I GLU* 5.5 1.0 - - - +
481I LEU* 3.6 21.9 - - - +
21L ARG* 3.3 13.7 + - - +
22L VAL* 4.3 3.1 - - - -
23L ALA 3.2 0.4 - - - -
24L THR* 1.3 78.6 + - - +
26L LEU* 1.3 60.0 + - - +
29L HIS* 2.8 42.9 + - - -
86L VAL* 4.4 11.4 - - - -
87L PRO* 5.5 2.0 - - - -
88L ARG* 3.6 22.4 + - - -
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Residues in contact with LEU 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L VAL* 4.5 28.5 - - + -
22L VAL* 3.2 22.1 + - + +
23L ALA* 3.0 9.0 + - - +
25L SER* 1.3 74.1 - - - +
27L ARG* 1.3 68.2 + - - +
29L HIS* 3.2 7.2 + - - +
30L ILE* 3.0 48.9 + - + +
39L PHE* 5.3 6.1 - - + -
42L VAL* 3.8 33.4 - - + -
71L VAL* 5.1 6.1 - - + -
83L VAL* 5.0 9.6 - - + -
86L VAL* 4.9 15.7 - - + +
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Residues in contact with ARG 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LYS* 5.9 1.0 - - - +
105B LYS* 4.1 30.7 - - - +
106B GLU* 5.2 5.5 + - - +
23L ALA* 2.9 23.0 + - - +
24L THR 4.3 3.1 - - - +
26L LEU* 1.3 76.7 - - + +
28L GLU* 1.3 63.1 + - + +
30L ILE* 3.2 21.9 + - + +
31L LYS* 3.3 13.7 + - - +
41L GLU* 2.3 40.6 + - - +
42L VAL* 2.8 39.5 + - + +
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Residues in contact with GLU 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LYS* 5.3 11.1 + - - -
481I LEU* 3.5 45.5 - - + +
482I GLY 4.9 3.1 - - - +
24L THR 3.3 19.3 + - - +
26L LEU 3.2 0.6 - - - -
27L ARG* 1.3 79.4 - - + +
29L HIS* 1.3 60.6 + - - +
31L LYS* 3.1 48.4 + - - +
32L LEU* 3.4 13.2 + - - +
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Residues in contact with HIS 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477I GLU* 2.5 37.4 + - - -
480I SER* 5.3 4.5 - - - -
481I LEU* 3.6 22.7 - - + +
25L SER* 2.8 33.1 + - - +
26L LEU* 3.6 7.0 - - - +
28L GLU* 1.3 74.1 - - - +
30L ILE* 1.3 63.8 + - + +
32L LEU* 3.4 6.9 + - + +
33L HIS* 2.6 52.2 + + + -
82L LEU* 5.0 9.1 - - + +
85L SER* 5.4 3.6 - - - -
86L VAL* 4.7 18.8 - - + -
87L PRO* 4.3 4.8 - - + +
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Residues in contact with ILE 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L LEU* 3.0 41.5 + - + +
27L ARG* 3.5 14.6 - - + +
28L GLU 3.2 0.6 - - - -
29L HIS* 1.3 77.1 - - - +
31L LYS* 1.3 58.2 + - - +
32L LEU 3.2 0.2 + - - -
33L HIS* 3.3 4.6 + - - +
34L ASN* 2.9 31.6 + - - -
39L PHE* 3.6 50.5 - - + +
42L VAL* 6.0 1.1 - - + -
82L LEU* 5.5 6.1 - - + -
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Residues in contact with LYS 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480I SER 5.0 4.6 + - - -
482I GLY 5.6 4.6 + - - +
27L ARG 3.3 5.6 + - - +
28L GLU* 3.1 41.0 + - - +
30L ILE* 1.3 80.4 - - + +
32L LEU* 1.3 78.6 + - + +
34L ASN* 2.9 22.6 - - - +
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Residues in contact with LEU 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63I SER* 3.4 47.8 - - - +
64I GLY* 4.6 3.1 - - - -
480I SER* 3.2 42.0 - - - +
481I LEU* 3.6 15.0 - - + -
28L GLU 3.4 11.1 + - - +
29L HIS* 3.7 12.8 - - + +
30L ILE 3.1 0.8 - - - -
31L LYS* 1.3 103.0 - - + +
33L HIS* 1.3 67.0 + - + +
34L ASN* 3.3 9.3 + - - -
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Residues in contact with HIS 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I SER* 5.7 2.9 - - - -
29L HIS* 2.6 46.8 + + - +
30L ILE* 4.2 2.2 - - - +
32L LEU* 1.3 82.0 - - + +
34L ASN* 1.3 71.5 + - - +
82L LEU* 3.5 39.9 - - + +
85L SER* 6.2 0.4 - - - -
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Residues in contact with ASN 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L ILE* 2.9 19.6 + - - -
31L LYS* 2.9 21.8 - - - +
32L LEU 4.1 8.2 + - - -
33L HIS* 1.3 82.1 - - - +
38L LEU* 5.9 2.9 - - - +
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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