Contacts of the helix formed by residues 111 - 128 (chain A) in PDB entry 1U61
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 ASN 111 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLU* 5.9 0.6 + - - -
106A HIS* 2.9 48.2 + - + +
109A LEU* 3.4 32.9 - - - +
110A ASN* 1.3 73.4 - - - +
112A ARG* 1.3 58.0 + - - +
113A GLU 3.4 2.7 - - - -
114A ARG* 3.5 9.5 + - + -
115A LEU* 2.9 29.6 + - - +
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Residues in contact with ARG 112 (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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22A GLN* 5.5 7.5 - - - +
23A TYR* 4.7 10.4 + - - +
110A ASN 3.1 9.1 + - - +
111A ASN* 1.3 74.0 - - - +
113A GLU* 1.3 55.0 + - - +
115A LEU* 3.2 7.9 + - - +
116A ASP* 2.8 53.3 + - - +
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Residues in contact with GLU 113 (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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111A ASN 3.4 0.6 - - - -
112A ARG* 1.3 78.7 - - - +
114A ARG* 1.3 63.2 + - - +
116A ASP* 3.4 10.2 + - + +
117A GLU* 3.1 41.0 + - + +
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Residues in contact with ARG 114 (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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64A PHE* 3.0 52.2 + - - -
65A LEU* 3.8 3.6 - - - +
66A THR* 4.3 7.8 - - - +
69A GLU* 2.8 43.3 + - - +
106A HIS* 3.8 14.4 - - + +
111A ASN* 3.5 17.3 + - + +
112A ARG 3.4 0.4 - - - -
113A GLU* 1.3 79.7 + - - +
115A LEU* 1.3 63.4 + - - +
117A GLU* 2.8 32.8 + - - +
118A ILE* 3.0 24.8 + - - +
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Residues in contact with LEU 115 (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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19A VAL* 4.0 20.2 - - + -
23A TYR* 3.7 18.4 - - + +
102A LEU 5.1 0.2 - - - +
103A ILE* 3.8 42.6 - - + +
106A HIS* 4.1 12.7 - - + +
107A HIS* 3.8 31.6 - - + +
111A ASN 2.9 18.2 + - - +
112A ARG* 3.5 8.1 - - - +
114A ARG* 1.3 75.1 - - - +
116A ASP* 1.3 66.0 + - - +
118A ILE* 3.2 6.1 + - + +
119A VAL* 2.9 31.1 + - + +
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 2.7 38.7 + - - -
112A ARG* 2.8 35.3 + - - +
113A GLU* 3.4 12.2 - - - +
115A LEU* 1.3 73.7 - - - +
117A GLU* 1.3 57.4 + - + +
120A TYR* 2.8 61.9 + - + -
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Residues in contact with GLU 117 (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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64A PHE* 4.1 10.2 - - + -
113A GLU* 3.1 33.5 + - + +
114A ARG* 2.8 44.8 + - - +
116A ASP* 1.3 79.3 - - + +
118A ILE* 1.3 55.9 + - - +
120A TYR* 4.3 3.0 - - - +
121A LYS* 3.0 31.0 + - - +
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Residues in contact with ILE 118 (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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55A VAL* 5.4 0.2 - - - +
59A LEU* 4.5 10.9 - - + +
64A PHE* 4.1 22.2 - - + -
65A LEU* 4.2 6.3 - - + -
69A GLU* 3.8 14.4 - - - +
99A PHE* 4.3 12.8 - - + -
102A LEU* 4.1 22.0 - - + -
103A ILE* 3.9 21.8 - - + -
106A HIS* 3.7 30.3 - - + -
114A ARG* 3.0 21.0 + - - +
115A LEU* 3.2 8.5 + - + +
117A GLU* 1.3 75.4 - - - +
119A VAL* 1.3 59.7 + - - +
121A LYS* 3.3 3.9 + - - +
122A ALA* 2.8 26.9 + - - +
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 4.2 18.2 - - + -
23A TYR* 3.5 52.7 - - + -
103A ILE* 4.0 25.6 - - + -
115A LEU* 2.9 26.3 + - + +
116A ASP 4.1 1.3 - - - +
118A ILE* 1.3 74.8 - - - +
120A TYR* 1.3 59.8 + - - +
122A ALA* 3.1 8.1 + - - +
123A ILE* 2.9 38.4 + - + +
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Residues in contact with TYR 120 (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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23A TYR* 4.0 23.6 - + - -
26A TYR* 6.2 0.7 - - - -
116A ASP* 2.8 57.4 + - + +
117A GLU* 4.3 2.9 - - - +
119A VAL* 1.3 73.9 - - - +
121A LYS* 1.3 60.5 + - - +
123A ILE* 3.4 18.6 + - + +
124A ALA* 3.0 23.7 + - - +
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Residues in contact with LYS 121 (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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58A HIS* 4.5 15.4 - - + -
59A LEU* 3.9 24.7 - - + -
64A PHE* 3.6 31.8 - - + -
117A GLU 3.0 20.8 + - - +
118A ILE* 3.5 4.7 - - - +
119A VAL 3.2 0.2 - - - -
120A TYR* 1.3 73.1 - - - +
122A ALA* 1.3 65.1 + - - +
124A ALA* 3.2 9.3 + - + +
125A VAL* 2.9 42.4 + - + +
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Residues in contact with ALA 122 (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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20A TYR* 4.2 10.3 - - + +
55A VAL* 3.6 36.0 - - + +
99A PHE* 4.0 16.4 - - + -
118A ILE 2.8 17.3 + - - +
119A VAL* 3.1 9.6 + - - +
121A LYS* 1.3 73.0 - - - +
123A ILE* 1.3 64.2 + - - +
125A VAL* 3.3 3.8 + - - +
126A LEU* 3.0 30.0 + - - +
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Residues in contact with ILE 123 (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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23A TYR* 4.9 3.6 - - + +
24A ILE* 3.7 31.2 - - + -
27A HIS* 3.7 46.4 - - + +
46A PHE* 4.1 10.7 - - + -
119A VAL* 2.9 31.9 + - + +
120A TYR* 3.7 20.9 - - + +
122A ALA* 1.3 76.4 - - + +
124A ALA* 1.3 57.5 + - - +
126A LEU* 3.3 2.3 + - - +
127A GLU* 3.0 40.5 + - - +
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Residues in contact with ALA 124 (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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120A TYR 3.0 16.7 + - - +
121A LYS* 3.2 12.3 + - + +
123A ILE* 1.3 74.9 - - - +
125A VAL* 1.3 66.3 + - + +
127A GLU* 3.3 6.1 + - - +
128A GLU* 3.0 26.1 + - - +
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Residues in contact with VAL 125 (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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54A LYS* 4.4 28.8 - - + -
55A VAL* 4.6 11.9 - - + -
58A HIS* 3.7 55.0 - - + +
59A LEU* 6.0 0.4 - - + -
121A LYS* 2.9 30.7 + - + +
122A ALA* 3.6 7.6 - - - +
124A ALA* 1.3 77.7 - - - +
126A LEU* 1.3 63.5 + - - +
127A GLU 3.4 0.2 + - - -
128A GLU* 3.4 22.3 + - - +
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Residues in contact with LEU 126 (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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20A TYR* 3.7 11.9 - - - +
45A SER 3.9 6.7 - - - +
46A PHE* 3.6 48.2 - - + +
51A ALA* 3.5 31.6 - - + +
54A LYS* 4.2 26.7 + - + +
55A VAL* 3.7 18.8 - - + -
122A ALA 3.0 16.6 + - - +
123A ILE 3.9 3.4 - - - +
125A VAL* 1.3 76.6 - - - +
127A GLU* 1.3 61.7 + - - +
128A GLU 4.3 3.6 - - - +
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Residues in contact with GLU 127 (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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27A HIS* 2.7 33.2 + - - -
31A LYS* 3.7 16.8 + - - +
46A PHE* 3.5 20.0 - - + -
123A ILE* 3.0 29.1 + - - +
124A ALA* 4.1 5.1 - - - +
126A LEU* 1.3 77.3 - - - +
128A GLU* 1.3 64.7 + - - +
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Residues in contact with GLU 128 (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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54A LYS* 5.1 6.6 + - - -
58A HIS* 5.4 6.1 + - - -
124A ALA 3.0 17.4 + - - +
125A VAL* 3.4 18.2 + - - +
126A LEU 4.3 2.9 - - - +
127A GLU* 1.3 81.4 - - - +
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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