Contacts of the helix formed by residues 85 - 97 (chain A) in PDB entry 1DGD
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 ARG 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LEU* 5.4 0.4 - - - +
84A SER* 1.3 77.2 - - - +
86A PRO* 1.3 62.8 - - + +
88A VAL* 3.4 4.1 + - - +
89A ASP* 2.8 46.1 + - - +
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Residues in contact with PRO 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A TYR* 3.7 34.8 - - + +
75A LEU* 4.4 5.4 - - + -
84A SER* 3.6 13.9 - - - +
85A ARG* 1.3 93.1 - - + +
87A VAL* 1.3 54.8 + - - +
89A ASP* 4.0 6.5 - - + +
90A LEU* 2.9 32.2 + - - +
308A PRO* 3.9 13.5 - - + +
311A ALA* 3.8 3.4 - - - +
312A ALA* 3.7 28.5 - - - +
315A LEU* 4.5 6.9 - - + +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A MET 5.9 0.2 - - - +
83A LEU* 4.3 14.6 - - + -
84A SER* 3.6 23.8 + - - +
85A ARG 3.3 0.2 - - - -
86A PRO* 1.3 77.0 - - - +
88A VAL* 1.3 60.2 + - + +
91A ALA* 2.9 31.1 + - + +
107A LEU* 3.7 23.4 - - + +
306A SER* 3.4 48.5 - - - +
307A ASP 3.9 11.7 - - - +
308A PRO* 4.6 0.2 - - + -
311A ALA* 4.0 4.7 - - + -
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 4.5 28.0 - - + -
84A SER 3.4 16.3 + - - +
85A ARG* 4.1 3.8 - - - +
87A VAL* 1.3 77.4 - - + +
89A ASP* 1.3 62.1 + - - +
91A ALA* 3.9 4.8 - - + +
92A THR* 2.7 43.0 + - - +
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Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ARG* 2.8 33.2 + - - +
86A PRO* 4.0 0.6 - - - +
88A VAL* 1.3 82.0 - - - +
90A LEU* 1.3 59.1 + - - +
92A THR* 3.9 5.0 - - - -
93A ARG* 2.9 28.4 + - - +
315A LEU* 3.4 27.6 - - + +
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PRO 2.9 18.8 + - - +
87A VAL 3.8 2.9 - - - +
89A ASP* 1.3 74.0 - - - +
91A ALA* 1.3 69.0 + - - +
93A ARG 3.3 0.5 + - - -
94A LEU* 2.9 31.7 + - + +
107A LEU* 4.1 24.2 - - + -
274A LEU* 4.9 5.8 - - + -
280A LEU* 3.9 19.7 - - + -
311A ALA* 3.6 32.3 - - - +
314A GLY 4.3 1.1 - - - -
315A LEU* 3.9 19.9 - - + +
318A LEU* 3.7 29.6 - - + -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A VAL* 2.9 20.1 + - + +
88A VAL* 3.9 5.4 - - + +
90A LEU* 1.3 79.8 - - - +
92A THR* 1.3 62.5 + - - +
94A LEU* 3.2 3.0 + - - +
95A ALA* 3.1 21.3 + - - +
103A ASP 5.1 1.2 - - - +
105A ALA* 4.2 33.7 + - + +
107A LEU* 4.6 7.3 - - + +
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Residues in contact with THR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A VAL* 2.7 31.6 + - - +
89A ASP* 3.9 5.8 - - - -
91A ALA* 1.3 74.6 - - - +
93A ARG* 1.3 65.4 + - - +
95A ALA* 3.0 10.5 + - + +
96A ASN* 2.9 36.0 + - - +
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Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ASP 2.9 19.6 + - - +
90A LEU* 3.3 4.7 + - - +
92A THR* 1.3 77.4 - - - +
94A LEU* 1.3 63.1 + - - +
96A ASN* 3.1 11.9 + - - +
97A ILE* 3.0 32.8 + - + +
315A LEU* 3.9 26.6 - - + +
318A LEU* 3.9 20.5 - - + +
319A ASP* 2.3 45.8 + - - +
322A GLN* 3.1 36.3 + - - +
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU* 2.9 30.8 + - + +
91A ALA 3.8 3.6 - - - +
92A THR 3.2 0.2 - - - -
93A ARG* 1.3 74.3 - - - +
95A ALA* 1.3 56.2 + - - +
97A ILE* 4.4 4.5 - - + -
98A THR* 2.5 40.1 + - + +
105A ALA* 4.2 16.4 - - + -
107A LEU* 4.3 8.7 - - + -
249A VAL* 6.4 0.4 - - + -
256A PHE* 4.7 11.2 - - + -
270A LEU* 3.7 24.5 - - + -
274A LEU* 4.8 9.2 - - + -
282A ALA* 4.2 25.1 - - + -
284A VAL* 4.4 13.9 - - + -
318A LEU* 4.4 16.6 - - + -
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ALA 3.1 10.4 + - - +
92A THR* 3.0 13.1 + - + +
94A LEU* 1.3 75.5 - - - +
96A ASN* 1.3 65.6 + - - +
98A THR* 3.1 5.6 + - - -
102A LEU 3.5 5.6 - - - +
103A ASP* 3.4 33.2 - - - +
105A ALA* 5.8 0.2 - - - +
284A VAL* 5.0 2.6 - - - +
435A NA 2.4 27.0 - - - -
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Residues in contact with ASN 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A THR* 2.9 36.9 + - - +
93A ARG* 3.1 12.0 + - - +
95A ALA* 1.3 82.8 - - - +
97A ILE* 1.3 64.9 + - + +
98A THR 3.4 3.6 - - - +
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ARG* 3.0 25.7 + - + +
94A LEU* 4.1 8.1 - - + +
96A ASN* 1.3 80.8 - - + +
98A THR* 1.3 64.6 + - - +
255A MET* 3.4 35.1 - - + +
256A PHE* 3.5 23.6 - - + -
259A GLN* 3.5 11.6 - - - +
318A LEU* 4.1 23.8 - - + -
322A GLN* 4.0 22.9 - - - +
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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