Contacts of the helix formed by residues 118 - 132 (chain L) in PDB entry 1DZH
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 118 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L PRO* 5.4 8.3 - - - +
113L GLU* 3.5 37.2 + - + +
115L THR* 3.1 40.4 + - - +
117L ASP* 1.3 89.9 + - - +
119L ILE* 1.3 68.9 + - - +
120L HIS 3.3 0.4 - - - -
121L PHE* 3.1 17.3 + - - +
122L PHE* 3.4 25.0 + - + -
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Residues in contact with ILE 119 (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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51L LEU* 4.7 4.8 - - + +
88L ALA* 5.7 0.4 - - + -
91L LYS* 4.5 5.4 - - - -
103L MET* 3.5 33.2 - - + -
108L PHE* 3.5 54.7 - - + +
111L ILE* 3.7 16.2 - - + -
113L GLU* 5.9 2.9 - - + -
115L THR 4.6 6.1 - - - +
116L SER 3.4 21.3 - - - +
118L GLN* 1.3 78.1 - - + +
120L HIS* 1.3 66.6 + - + +
122L PHE* 2.9 20.0 + - + +
123L PHE* 3.0 17.9 + - + -
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Residues in contact with HIS 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L MET* 5.5 3.7 + - + +
19L PRO* 5.1 5.1 - - + +
88L ALA* 3.9 9.8 + - + -
91L LYS* 2.9 40.9 + - - -
92L LEU* 3.5 44.3 + - + +
116L SER 3.4 10.8 - - - -
117L ASP* 3.5 19.8 + - + +
118L GLN 3.3 0.4 - - - -
119L ILE* 1.3 74.2 - - + +
121L PHE* 1.3 61.6 + - - +
123L PHE* 4.4 1.1 - - - -
124L ALA* 3.2 10.4 + - - +
161L ILE* 5.6 0.2 - - + -
165L VAL* 3.1 34.4 - - + +
166L TYR* 3.1 27.1 - - - +
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Residues in contact with PHE 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L ILE 5.2 5.2 - - - -
8L CYS 5.7 2.9 - - - -
10L ALA* 3.6 32.3 - - + -
11L LYS 3.6 20.9 - - - -
12L PRO* 3.8 32.8 - - + +
15L ILE* 5.7 5.8 - - - -
17L MET* 5.8 8.1 - - + +
44L THR* 4.8 13.7 - - + -
117L ASP 4.4 4.3 + - - +
118L GLN* 3.1 17.0 + - - +
119L ILE 3.1 0.2 + - - -
120L HIS* 1.3 75.6 - - - +
122L PHE* 1.3 79.5 + + + +
124L ALA* 3.5 7.0 - - + +
125L LYS* 3.1 31.7 + - + +
165L VAL* 5.3 3.8 - - - +
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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
----------------------------------------------------------
12L PRO* 5.8 4.0 - - + -
44L THR* 4.9 3.8 - - + -
47L ARG* 3.5 61.2 - - + +
48L VAL* 4.4 5.5 - - + +
51L LEU* 4.1 9.4 - - + -
111L ILE* 4.1 24.9 - - + -
113L GLU* 4.0 24.2 - - + -
118L GLN* 3.4 32.5 - - + -
119L ILE* 2.9 9.1 + - + +
121L PHE* 1.3 94.9 - + + +
123L PHE* 1.3 56.7 + - - +
125L LYS* 2.8 9.4 + - - +
126L LEU* 2.7 33.8 + - - +
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Residues in contact with PHE 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51L LEU* 3.4 21.5 - - + +
55L ASN* 4.3 8.3 - - - -
81L LEU* 4.6 6.3 - - + -
84L SER* 3.9 9.0 - - - -
85L THR* 3.1 42.0 - - - -
88L ALA* 3.8 30.7 - - + -
108L PHE* 3.9 23.8 - + - -
119L ILE* 3.0 17.3 + - + +
120L HIS* 4.0 1.3 - - - +
122L PHE* 1.3 75.0 - - - +
124L ALA* 1.3 52.5 + - - +
126L LEU* 3.2 12.5 + - + +
127L ASN* 2.8 57.7 + - - -
166L TYR* 3.8 17.5 - + + +
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Residues in contact with ALA 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L ILE 5.6 5.6 - - - +
120L HIS 3.2 16.9 + - - +
121L PHE* 3.5 8.7 - - + +
123L PHE* 1.3 75.9 - - - +
125L LYS* 1.3 50.5 + - - +
127L ASN* 3.2 10.5 + - - +
128L CYS* 2.8 41.5 + - - -
164L LEU 5.6 0.4 - - - +
165L VAL* 3.2 35.1 - - + +
166L TYR* 4.7 0.2 - - - -
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Residues in contact with LYS 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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8L CYS* 5.4 7.6 - - - +
44L THR* 6.4 1.8 - - + -
48L VAL* 4.1 15.5 - - + -
121L PHE* 3.1 23.1 + - + +
122L PHE* 2.8 15.7 + - - +
124L ALA* 1.3 67.0 - - - +
126L LEU* 1.3 63.3 + - - +
128L CYS* 3.0 12.8 + - + +
129L ARG* 2.9 38.9 + - - +
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Residues in contact with LEU 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48L VAL* 3.7 30.0 - - + +
51L LEU* 3.7 16.2 - - + -
52L SER* 4.9 3.4 - - - +
55L ASN* 3.6 27.1 - - - +
81L LEU* 4.7 2.0 - - + -
122L PHE 2.7 14.7 + - - +
123L PHE* 3.3 16.8 - - + +
125L LYS* 1.3 68.8 - - - +
127L ASN* 1.3 64.4 + - - +
129L ARG* 3.0 6.5 + - - +
130L LEU* 2.9 49.6 + - + +
417L LEU* 4.3 13.7 - - + +
419L THR* 4.1 21.5 - - + -
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Residues in contact with ASN 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81L LEU* 5.2 0.3 - - - +
85L THR* 4.1 7.4 + - - +
123L PHE* 2.8 53.5 + - - -
124L ALA* 3.4 9.3 - - - +
126L LEU* 1.3 72.0 - - - +
128L CYS* 1.3 55.7 + - - +
130L LEU* 4.4 6.4 - - - +
131L TYR* 3.0 65.0 + - + +
144L ASN* 5.5 3.4 - - - +
165L VAL 4.9 1.4 + - - +
166L TYR* 3.8 21.4 - - - +
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Residues in contact with CYS 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L ILE 4.6 2.2 - - - -
8L CYS* 2.0 61.7 - - + -
124L ALA* 2.8 30.7 + - - -
125L LYS* 3.1 12.3 - - - +
127L ASN* 1.3 71.1 - - - +
129L ARG* 1.3 73.2 + - - +
132L ARG* 3.0 32.7 + - - +
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Residues in contact with ARG 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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8L CYS* 5.1 14.0 + - - +
45L ASN* 4.5 20.0 + - - +
48L VAL* 4.7 12.4 - - - +
125L LYS* 2.9 39.3 + - - +
126L LEU* 3.6 6.5 - - - +
128L CYS* 1.3 83.4 - - - +
130L LEU* 1.3 64.1 + - - +
132L ARG 3.9 1.2 + - - -
133L LYS* 3.2 30.9 - - - +
417L LEU* 3.5 35.0 - - + -
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Residues in contact with LEU 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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81L LEU* 3.9 29.6 - - + -
126L LEU* 2.9 45.0 + - + +
127L ASN* 3.9 5.8 - - - +
129L ARG* 1.3 74.6 - - - +
131L TYR* 1.3 80.6 + - + +
132L ARG 3.7 0.2 + - - -
133L LYS* 4.6 10.3 + - - +
140L LEU* 4.1 22.6 - - + +
414L GLU* 4.2 16.3 - - + +
417L LEU* 3.5 21.3 - - + -
419L THR* 3.3 22.9 - - - +
421L ILE* 5.5 1.3 - - + -
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Residues in contact with TYR 131 (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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81L LEU* 3.3 26.7 - - + +
85L THR* 5.1 2.3 + - - -
127L ASN* 3.0 56.6 + - + +
128L CYS 4.0 0.4 - - - -
130L LEU* 1.3 83.1 - - + +
132L ARG* 1.3 58.5 + - - +
133L LYS 3.8 1.7 + - - -
140L LEU* 3.7 48.4 - - + +
141L VAL* 3.7 16.4 - - - +
142L SER* 3.5 31.8 + - - +
219L ILE* 3.8 13.6 - - + +
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Residues in contact with ARG 132 (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 CYS* 5.3 7.2 - - - -
128L CYS* 3.0 24.1 + - - +
129L ARG* 4.3 1.0 - - - +
130L LEU 3.5 1.0 - - - -
131L TYR* 1.3 78.2 - - - +
133L LYS* 1.3 63.9 + - - +
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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
------------------------------------------------------------
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