Contacts of the helix formed by residues 120 - 130 (chain L) in PDB entry 5MS0
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 HIS 120 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108L ILE* 4.4 12.9 - - + +
112L LYS* 3.8 25.8 - - + -
118L ASP 2.8 10.4 + - - +
119L SER* 1.3 75.2 - - - +
121L LYS* 1.3 62.6 + - - +
122L PHE 3.2 1.3 - - - -
123L VAL* 4.0 3.4 - - - +
124L ASN* 2.9 29.7 + - - +
10R U 4.8 23.1 - - + +
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Residues in contact with LYS 121 (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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118L ASP* 5.0 7.0 - - + +
119L SER 4.9 0.4 - - - +
120L HIS* 1.3 76.9 - - - +
122L PHE* 1.3 58.4 + - - +
124L ASN* 3.7 6.7 - - - +
125L GLY 2.9 17.8 + - - -
10R U 4.9 3.9 + - - +
11R U 3.9 20.4 - - - +
12R U 2.9 39.6 + - - +
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Residues in contact with PHE 122 (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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118L ASP* 6.2 0.2 - - - +
119L SER* 4.3 19.7 - - - +
120L HIS 3.2 0.8 - - - +
121L LYS* 1.3 77.4 - - - +
123L VAL* 1.3 57.9 + - - +
125L GLY* 3.0 5.4 + - - -
126L VAL* 2.9 24.7 + - - +
12R U 4.3 21.5 + - - +
13R A 4.7 21.5 - - + +
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Residues in contact with VAL 123 (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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108L ILE* 5.0 14.4 - - + -
111L ALA* 5.6 5.2 - - + -
119L SER 4.0 14.1 + - - +
120L HIS* 3.7 4.9 + - - +
122L PHE* 1.3 79.4 - - - +
124L ASN* 1.3 56.1 + - - +
126L VAL* 3.0 9.8 + - + +
127L LEU* 2.9 34.4 + - + +
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Residues in contact with ASN 124 (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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108L ILE* 5.9 2.4 - - + +
120L HIS 2.9 22.0 + - - +
121L LYS* 3.7 8.1 - - - +
122L PHE 3.2 0.2 - - - -
123L VAL* 1.3 76.5 - - - +
125L GLY* 1.3 59.5 + - - +
127L LEU* 4.9 1.1 - - - +
128L ASP* 4.0 12.5 + - - +
9R C 5.7 6.5 - - + +
10R U 4.6 9.0 - - - +
11R U 3.0 40.8 + - + +
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Residues in contact with GLY 125 (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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121L LYS 2.9 16.1 + - - -
122L PHE 3.0 5.6 + - - -
124L ASN* 1.3 77.0 - - - +
126L VAL* 1.3 62.3 + - - +
128L ASP* 4.5 1.2 - - - +
129L LYS* 4.2 12.0 + - - +
11R U 3.7 12.1 + - - -
12R U 3.8 38.2 + - - +
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Residues in contact with VAL 126 (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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69L TYR* 5.8 11.8 - - + +
85L LEU* 6.5 1.1 - - + -
122L PHE 2.9 10.9 + - - +
123L VAL* 3.0 13.8 + - + +
125L GLY* 1.3 78.5 - - - +
127L LEU* 1.3 61.8 + - + +
129L LYS* 3.1 8.5 + - - +
130L ALA* 2.9 26.6 + - + +
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Residues in contact with LEU 127 (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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88L ALA* 6.6 0.2 - - + -
104L ILE* 5.7 10.1 - - + -
123L VAL 2.9 14.1 + - - +
124L ASN* 5.5 0.9 - - - +
126L VAL* 1.3 77.8 - - + +
128L ASP* 1.3 58.2 + - - +
130L ALA* 3.6 13.2 - - + +
131L ALA* 3.1 23.4 + - - +
9R C 6.0 2.7 - - + -
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Residues in contact with ASP 128 (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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124L ASN 4.0 17.1 + - - +
125L GLY 5.0 2.0 - - - +
126L VAL 3.2 1.2 - - - -
127L LEU* 1.3 78.9 - - - +
129L LYS* 1.3 59.9 + - - +
130L ALA 3.2 0.2 - - - -
131L ALA* 3.5 17.2 + - - +
132L PRO* 4.5 2.3 - - - +
9R C 5.3 14.8 - - + +
11R U 4.5 16.4 - - - +
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Residues in contact with LYS 129 (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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69L TYR* 6.5 1.1 - - + -
125L GLY 4.2 9.4 + - - +
126L VAL 3.1 8.9 + - - +
128L ASP* 1.3 76.9 - - - +
130L ALA* 1.3 59.6 + - - +
131L ALA 3.2 3.2 + - - -
132L PRO* 3.9 13.6 - - - +
133L VAL* 4.8 1.4 + - - -
12R U 5.4 4.3 - - - +
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Residues in contact with ALA 130 (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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65L LEU 5.8 4.3 - - - +
92L LEU* 6.1 1.0 - - - +
126L VAL* 2.9 17.4 + - + +
127L LEU* 3.6 13.7 + - + -
128L ASP 3.2 0.4 - - - -
129L LYS* 1.3 75.5 - - - +
131L ALA* 1.3 61.6 + - - +
132L PRO 3.5 0.4 - - - -
133L VAL* 3.3 23.3 - - + +
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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
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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