Contacts of the helix formed by residues 95 - 105 (chain A) in PDB entry 1ULH
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 ASP 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A SER* 5.9 0.4 - - - -
93A HIS* 3.6 4.9 + - - -
94A ARG* 1.3 70.3 - - - +
96A MET* 1.3 65.0 + - - +
97A ASN* 3.0 18.9 + - - +
98A GLN* 2.9 46.2 + - + +
99A VAL* 3.3 8.3 + - - +
257A GLN* 4.7 0.7 - - - +
274A ARG* 2.7 40.9 + - - +
284A LYS* 4.7 3.8 - - - +
286A ALA* 4.0 11.4 - - + -
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Residues in contact with MET 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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69A LEU* 4.8 11.2 - - + -
73A ILE* 5.3 10.5 - - + -
93A HIS* 3.2 27.3 - - + +
94A ARG 3.5 2.2 + - - -
95A ASP* 1.3 75.2 - - - +
97A ASN* 1.3 56.1 + - - +
99A VAL* 3.3 24.0 + - + +
100A LEU* 2.9 61.9 + - + +
109A PHE* 5.3 0.2 - - + -
136A LEU* 5.4 0.7 - - + -
140A PHE* 4.4 16.2 - - + -
259A LEU* 3.6 35.7 - - + -
286A ALA* 4.6 1.8 - - - -
287A LEU 4.9 0.4 - - - +
288A LEU* 3.9 22.2 - - + -
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Residues in contact with ASN 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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69A LEU* 5.4 5.9 - - + +
72A ARG* 4.0 10.2 + - - +
93A HIS* 4.0 10.6 + - - +
95A ASP* 3.4 20.3 + - - +
96A MET* 1.3 80.8 + - - +
98A GLN* 1.3 69.1 + - - +
100A LEU* 3.2 12.7 + - - +
101A ASP* 2.8 45.7 + - - +
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Residues in contact with GLN 98 (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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95A ASP* 2.9 30.3 + - + +
97A ASN* 1.3 85.1 + - - +
99A VAL* 1.3 63.5 + - - +
101A ASP* 3.4 12.9 - - + +
102A ALA* 3.5 19.2 + - - +
257A GLN* 2.9 40.6 + - - +
283A PRO* 5.3 4.6 - - - +
284A LYS* 4.3 10.7 + - - +
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Residues in contact with VAL 99 (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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95A ASP 3.7 3.8 - - - +
96A MET* 3.3 22.9 + - + +
97A ASN 3.2 0.2 - - - -
98A GLN* 1.3 73.6 - - - +
100A LEU* 1.3 66.6 - - - +
102A ALA* 3.3 6.8 + - - +
103A TYR* 3.2 19.2 + - - +
109A PHE* 3.5 47.6 - - + +
140A PHE* 6.1 0.2 - - + -
257A GLN* 3.5 22.7 - - + -
259A LEU* 4.4 7.0 - - + -
286A ALA* 3.3 33.9 - - + -
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Residues in contact with LEU 100 (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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69A LEU* 4.0 19.3 - - + -
72A ARG* 3.4 43.5 - - + +
73A ILE* 4.4 20.4 - - + -
76A ALA* 4.9 5.6 - - + -
96A MET* 2.9 45.1 + - + +
97A ASN* 3.4 8.3 - - - +
99A VAL* 1.3 78.4 - - - +
101A ASP* 1.3 62.9 + - - +
103A TYR* 3.0 16.2 + - + +
104A GLU* 3.2 20.1 + - - +
140A PHE* 4.2 20.2 - - + -
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Residues in contact with ASP 101 (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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72A ARG* 3.4 17.0 + - - +
97A ASN* 2.8 38.9 + - - +
98A GLN* 3.4 14.1 - - + +
99A VAL 3.3 0.2 - - - -
100A LEU* 1.3 72.7 - - - +
102A ALA* 1.3 58.6 + - - +
104A GLU* 3.2 7.3 - - - +
105A ASN* 2.7 40.1 + - - +
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Residues in contact with ALA 102 (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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98A GLN 3.5 8.6 + - - +
99A VAL* 3.3 9.2 + - - +
100A LEU 3.2 0.6 - - - -
101A ASP* 1.3 78.2 - - - +
103A TYR* 1.3 59.9 + - - +
105A ASN* 3.4 5.6 + - - +
106A LYS 3.3 4.0 + - - -
107A LYS* 2.6 60.6 + - + +
108A PRO 4.6 6.3 - - - +
109A PHE* 5.7 1.8 - - + -
257A GLN* 6.0 4.0 - - + -
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Residues in contact with TYR 103 (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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76A ALA* 3.8 39.2 + - + -
77A THR 4.8 0.2 - - - -
99A VAL 3.2 11.8 + - - +
100A LEU* 3.0 15.4 + - + +
102A ALA* 1.3 77.4 - - - +
104A GLU* 1.3 59.5 + - - +
106A LYS* 3.5 2.6 + - - -
107A LYS 3.7 3.1 + - - -
109A PHE* 3.9 21.5 - + + -
139A VAL 3.7 5.6 + - - -
140A PHE* 2.6 67.7 + + + -
142A VAL* 4.4 2.9 - - + -
422A ASP* 3.6 8.0 + - - -
424A GLN* 2.7 67.4 + - - +
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Residues in contact with GLU 104 (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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72A ARG* 2.7 37.4 + - - -
75A ARG* 5.6 2.8 + - - -
76A ALA* 4.2 19.4 - - + +
100A LEU* 3.2 16.4 - - - +
101A ASP* 3.2 18.5 - - - +
103A TYR* 1.3 72.2 - - - +
105A ASN* 1.3 60.1 + - - +
106A LYS* 2.8 23.7 + - - +
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Residues in contact with ASN 105 (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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101A ASP* 2.7 34.6 + - - +
102A ALA* 3.4 6.8 + - - +
104A GLU* 1.3 75.1 - - - +
106A LYS* 1.3 69.4 + - - +
107A LYS* 3.5 29.0 + - - +
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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