Contacts of the helix formed by residues 8 - 20 (chain L) in PDB entry 6PSU
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 GLN 8 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7L SER* 1.3 73.3 - - - +
9L LEU* 1.3 69.9 + - + +
10L LYS 4.2 0.2 - - - +
11L LEU* 3.1 7.9 + - - +
12L LEU 2.9 21.0 + - - -
30L HIS* 3.1 61.2 + - - +
31L LEU 4.5 10.3 - - - +
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Residues in contact with LEU 9 (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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8L GLN* 1.3 77.9 - - + +
10L LYS* 1.3 61.3 + - - +
12L LEU* 3.0 15.6 - - + +
13L VAL* 2.9 36.0 + - - +
30L HIS 3.6 9.6 - - - +
31L LEU* 3.2 34.3 - - + -
44L ILE* 3.9 21.3 - - + -
84L LEU* 3.9 31.4 - - + +
87L VAL* 4.3 25.8 - - + +
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Residues in contact with LYS 10 (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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7L SER* 4.0 26.5 - - - +
8L GLN 3.3 0.8 - - - +
9L LEU* 1.3 78.1 - - - +
11L LEU* 1.3 57.3 + - - +
13L VAL* 3.0 16.4 - - + +
14L THR* 2.7 36.3 + - - +
17L LYS* 5.6 2.9 - - - +
78L GLU* 3.8 23.2 + - - -
81L ALA* 4.2 15.9 + - + +
84L LEU* 4.1 6.4 + - + +
85L SER* 5.0 13.0 - - - -
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Residues in contact with LEU 11 (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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7L SER* 3.0 23.4 + - - +
8L GLN* 3.1 10.8 + - - +
10L LYS* 1.3 79.5 - - - +
12L LEU* 1.3 56.7 + - - +
14L THR* 3.2 14.2 + - + -
15L ARG* 2.8 29.8 + - + +
18L GLU* 5.2 3.1 - - - +
30L HIS* 3.7 17.7 - - + +
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Residues in contact with LEU 12 (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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8L GLN 2.9 6.9 + - - -
9L LEU* 3.0 51.5 + - + +
11L LEU* 1.3 77.0 - - - +
13L VAL* 1.3 66.7 + - + +
15L ARG* 3.3 5.2 + - - +
16L GLY* 2.8 22.5 + - - -
22L LEU* 3.8 1.2 - - - +
26L GLU* 3.2 23.2 - - - +
27L VAL* 5.7 5.8 - - + -
30L HIS* 3.1 33.6 - - + +
31L LEU* 3.7 14.8 - - + -
44L ILE* 5.2 4.5 - - + -
48L ILE* 3.2 32.5 - - + -
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Residues in contact with VAL 13 (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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9L LEU 2.9 15.1 + - - +
10L LYS* 3.0 32.8 - - + +
12L LEU* 1.3 88.9 - - + +
14L THR* 1.3 61.1 + - - +
16L GLY* 3.2 1.4 + - - +
17L LYS* 2.9 49.8 + - - +
48L ILE* 4.6 2.5 - - + -
51L MET* 4.0 17.9 - - + -
53L ILE* 4.5 6.6 - - - +
81L ALA* 5.2 3.1 - - + -
84L LEU* 3.3 36.6 - - + -
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Residues in contact with THR 14 (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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10L LYS* 2.7 26.1 + - - +
11L LEU* 3.2 16.8 + - + -
13L VAL* 1.3 77.3 - - - +
15L ARG* 1.3 56.3 + - - +
17L LYS* 3.3 17.0 + - + +
18L GLU* 2.9 51.4 + - + +
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Residues in contact with ARG 15 (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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11L LEU* 2.8 16.3 + - + +
12L LEU* 3.3 9.2 - - - +
14L THR* 1.3 76.3 - - - +
16L GLY* 1.3 56.9 + - - +
18L GLU* 3.0 17.8 + - - +
19L GLN* 2.9 67.9 + - - +
22L LEU* 4.2 2.7 - - + +
26L GLU* 3.6 35.5 + - - +
30L HIS* 3.6 26.7 + - - +
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Residues in contact with GLY 16 (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 LEU 2.8 11.1 + - - -
13L VAL 3.2 4.6 + - - -
15L ARG* 1.3 75.4 - - - +
17L LYS* 1.3 57.3 + - - +
20L GLY* 2.7 33.3 + - - -
22L LEU* 3.2 28.0 - - - +
52L GLY 5.6 0.2 - - - +
53L ILE* 4.2 18.0 - - - +
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Residues in contact with LYS 17 (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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10L LYS* 5.6 3.0 - - - +
13L VAL* 2.9 47.6 + - - +
14L THR* 3.7 14.9 + - + +
16L GLY* 1.3 75.5 - - - +
18L GLU* 1.3 62.2 + - - +
20L GLY* 4.6 1.1 + - - -
51L MET* 3.9 32.2 - - + -
52L GLY 5.6 3.1 - - - +
53L ILE* 5.1 1.6 - - + -
77L ALA* 5.4 8.5 + - + -
78L GLU* 5.8 1.4 + - - -
81L ALA* 5.7 3.0 - - - +
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Residues in contact with GLU 18 (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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11L LEU* 5.2 4.6 - - - +
14L THR* 2.9 45.2 + - + +
15L ARG* 3.0 24.3 + - - +
16L GLY 3.1 0.4 - - - -
17L LYS* 1.3 80.4 - - - +
19L GLN* 1.3 67.2 + - + +
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Residues in contact with GLN 19 (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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165I HIS* 4.3 28.8 - - - +
166I SER* 5.7 7.0 - - - -
15L ARG* 2.9 61.7 + - - +
18L GLU* 1.3 80.6 + - + +
20L GLY* 1.3 64.2 + - - +
21L TYR* 3.3 15.8 + - + +
22L LEU* 3.1 16.7 - - + +
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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
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16L GLY* 2.7 26.6 + - - -
17L LYS 5.2 1.3 - - - -
18L GLU 3.6 0.8 - - - -
19L GLN* 1.3 72.3 - - - +
21L TYR* 1.3 62.0 + - - +
53L ILE* 2.7 23.8 - - - +
54L GLN* 3.8 12.1 - - - +
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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