Contacts of the helix formed by residues 95 - 105 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B SER* 5.2 0.2 + - - -
93B HIS* 3.6 7.5 + - - -
94B ARG* 1.3 71.6 - - - +
96B MET* 1.3 60.4 + - - +
97B ASN* 3.1 5.4 - - - +
98B GLN* 2.9 54.2 + - + +
99B VAL 3.2 8.3 + - - -
257B GLN* 5.4 1.3 - - - +
274B ARG* 2.8 38.4 + - - +
284B LYS* 4.8 7.6 - - - +
285B PRO 5.7 0.2 - - - -
286B ALA* 3.8 12.0 - - + +
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Residues in contact with MET 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 4.1 21.8 - - + -
73B ILE* 4.4 14.1 - - + -
93B HIS* 3.2 29.0 + - + +
94B ARG 3.1 4.9 + - - -
95B ASP* 1.3 77.1 - - - +
97B ASN* 1.3 57.2 + - - +
99B VAL* 2.9 18.6 + - + +
100B LEU* 2.9 35.9 + - + +
136B LEU* 5.2 2.5 - - + -
140B PHE* 4.6 18.6 - - + -
259B LEU* 3.9 30.7 - - + -
286B ALA* 4.9 0.2 - - - -
287B LEU 4.9 0.7 - - - +
288B LEU* 3.9 31.2 - - + -
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Residues in contact with ASN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 3.7 29.4 - - - +
72B ARG* 3.9 16.0 + - - +
93B HIS* 4.6 7.0 - - + -
95B ASP* 4.9 1.8 - - - -
96B MET* 1.3 81.2 - - - +
98B GLN* 1.3 53.4 + - + +
100B LEU* 3.7 8.3 - - - +
101B ASP* 2.7 42.1 + - - +
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Residues in contact with GLN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASP* 2.9 46.3 + - + +
97B ASN* 1.3 77.4 - - + +
99B VAL* 1.3 63.2 + - - +
100B LEU 3.2 0.4 - - - -
101B ASP* 3.4 17.1 - - + +
102B ALA* 3.2 21.0 + - - +
257B GLN* 3.8 20.0 + - - +
284B LYS* 5.6 2.6 + - - +
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASP 3.2 2.1 + - - +
96B MET* 2.9 19.8 + - + +
98B GLN* 1.3 76.3 - - - +
100B LEU* 1.3 61.4 + - + +
102B ALA* 3.5 3.4 + - - +
103B TYR* 2.9 26.0 + - + +
109B PHE* 3.7 41.2 - - + -
140B PHE* 5.6 1.6 - - + -
257B GLN* 3.7 22.9 - - + -
259B LEU* 4.2 18.6 - - + -
286B ALA* 3.4 33.0 - - + -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 4.7 1.6 - - + +
72B ARG* 3.2 48.1 + - + +
73B ILE* 3.6 26.0 - - + -
76B ALA* 3.8 29.3 - - + +
96B MET* 2.9 26.7 + - + +
97B ASN* 3.8 8.5 - - - +
99B VAL* 1.3 76.8 - - + +
101B ASP* 1.3 65.1 + - - +
102B ALA 3.1 2.0 - - - -
103B TYR* 4.0 3.8 - - + +
104B GLU* 3.1 23.0 + - - +
140B PHE* 4.1 25.4 - - + -
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ARG* 3.3 12.6 + - - +
97B ASN* 2.7 26.8 + - - +
98B GLN* 3.4 20.4 - - + +
100B LEU* 1.3 79.0 - - - +
102B ALA* 1.3 58.8 + - - +
104B GLU* 3.9 3.0 - - - +
105B ASN* 3.3 27.9 + - - +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLN 3.2 12.2 + - - +
99B VAL* 3.9 4.5 - - - +
100B LEU 3.1 0.2 - - - -
101B ASP* 1.3 78.4 - - - +
103B TYR* 1.3 65.4 + - - +
104B GLU 3.2 2.0 - - - -
105B ASN* 3.1 10.2 + - - +
107B LYS* 3.0 51.7 + - + +
108B PRO 4.7 4.9 - - - +
109B PHE* 5.8 1.1 - - + -
257B GLN* 5.2 10.3 - - + +
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Residues in contact with TYR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ALA* 3.1 38.2 + - + -
77B THR* 4.4 1.5 - - + +
99B VAL 2.9 21.7 + - - +
100B LEU* 4.0 7.0 - - - +
102B ALA* 1.3 72.4 - - - +
104B GLU* 1.3 65.6 + - - +
106B LYS* 3.3 15.1 + - - +
107B LYS 3.9 8.0 + - - -
108B PRO* 6.1 2.0 - - + -
109B PHE* 4.0 15.7 - + + -
139B VAL 3.8 6.6 + - - -
140B PHE* 3.5 68.4 + + + -
142B VAL* 4.9 2.7 - - + -
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ARG* 3.8 25.9 + - - +
76B ALA* 6.0 4.9 - - + +
100B LEU 3.1 15.4 + - - +
101B ASP* 3.9 2.6 - - - +
103B TYR* 1.3 83.8 - - - +
105B ASN* 1.3 71.2 + - - +
106B LYS* 3.2 11.7 + - - +
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Residues in contact with ASN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ASP 3.3 18.0 + - - +
102B ALA* 3.1 9.2 + - - +
104B GLU* 1.3 94.6 + - - +
106B LYS* 1.3 72.6 + - - +
107B LYS* 3.3 33.5 + - + +
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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