Contacts of the helix formed by residues 108 - 122 (chain B) in PDB entry 4Y1L
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 THR 108 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ARG* 4.3 1.3 + - - +
12B GLU* 3.0 33.4 - - - +
15B ALA* 6.4 2.0 - - + -
68B TYR* 5.5 0.2 - - - -
106B ALA 3.8 6.2 + - - -
107B ILE* 1.3 74.9 - - - +
109B ILE* 1.3 65.5 + - - +
110B LYS* 4.0 19.1 - - + +
111B GLN* 2.8 25.6 + - - +
112B ILE* 3.1 26.1 + - - +
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 4.3 1.1 - - + -
12B GLU* 2.9 33.2 + - + +
16B TRP* 5.1 4.7 - - + -
26B ALA* 4.5 12.3 - - + -
41B TRP* 3.6 36.1 - - + -
43B CYS* 5.4 0.2 - - - -
62B MET* 3.9 20.0 - - + -
64B PHE* 3.5 32.8 - - + -
68B TYR* 4.3 6.3 - - - +
108B THR* 1.3 70.8 - - - +
110B LYS* 1.3 57.4 + - - +
112B ILE* 3.2 11.6 + - + +
113B LEU* 3.0 40.5 + - + +
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA 5.4 1.0 + - - -
16B TRP* 4.1 22.0 - - + +
19B ASP* 3.8 33.2 + - - +
20B HIS* 4.4 1.0 - - - +
21B PRO* 3.9 31.1 - - + +
108B THR* 4.0 14.2 - - + +
109B ILE* 1.3 79.9 - - - +
111B GLN* 1.3 59.6 + - + +
113B LEU* 3.3 3.1 + - - +
114B LEU* 2.9 49.5 + - + +
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Residues in contact with GLN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE* 4.7 4.4 - - + +
104B ARG* 4.7 11.9 + - - +
106B ALA 3.7 3.2 + - - +
107B ILE* 3.2 20.7 - - + +
108B THR* 2.8 44.0 + - - +
110B LYS* 1.3 81.7 - - + +
112B ILE* 1.3 58.5 + - - +
114B LEU* 3.5 9.4 + - + +
115B GLY* 2.9 26.0 + - - -
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Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B MET* 3.6 18.2 - - + -
68B TYR* 5.7 1.1 - - - +
73B PRO* 3.7 35.4 - - + -
75B CYS* 4.1 7.4 - - - -
94B LEU* 4.9 1.0 - - - +
96B ILE* 4.2 9.4 - - + -
97B LEU* 3.5 27.6 - - + -
103B TRP* 4.2 11.4 - - + -
107B ILE* 3.7 12.8 - - + +
108B THR 3.1 16.7 + - - +
109B ILE* 3.4 16.6 - - + +
111B GLN* 1.3 75.9 - - - +
113B LEU* 1.3 57.8 + - - +
115B GLY* 3.1 2.8 + - - -
116B ILE* 2.9 39.3 + - + +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 3.7 30.3 - - + -
24B PHE* 4.0 18.6 - - + -
25B VAL 4.1 15.3 - - - +
26B ALA* 4.2 8.7 - - + -
43B CYS* 4.3 4.7 - - + -
44B ALA 5.1 0.7 - - - +
45B ILE* 3.8 28.6 - - + +
60B LEU* 4.1 17.0 - - + -
62B MET* 3.7 20.6 - - + -
109B ILE* 3.0 23.7 + - + +
110B LYS* 3.8 4.0 - - - +
112B ILE* 1.3 76.2 - - - +
114B LEU* 1.3 57.4 + - - +
116B ILE* 3.3 4.2 + - + +
117B GLN* 3.0 28.4 + - - +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PRO* 4.2 16.6 - - + -
24B PHE* 3.7 27.8 - - + -
110B LYS* 2.9 41.7 + - + +
111B GLN* 3.8 9.0 - - + +
113B LEU* 1.3 75.0 - - - +
115B GLY* 1.3 59.2 + - - +
117B GLN* 3.2 12.8 + - - +
118B GLU* 2.9 28.5 + - - +
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Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 4.3 13.2 - - - +
96B ILE* 5.4 3.8 - - - -
111B GLN 2.9 15.7 + - - -
112B ILE* 3.1 4.5 + - - -
114B LEU* 1.3 75.4 - - - +
116B ILE* 1.3 57.2 + - - +
118B GLU* 3.3 16.6 + - - +
119B LEU* 2.9 26.5 + - - +
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 3.7 16.6 - - + -
60B LEU* 3.9 22.9 - - + -
75B CYS* 4.1 24.0 - - + -
77B PHE* 4.0 22.9 - - + -
92B VAL* 4.3 14.4 - - + -
94B LEU* 4.0 15.9 - - + -
97B LEU* 4.2 6.1 - - + -
112B ILE* 2.9 20.9 + - + +
113B LEU* 3.7 7.6 - - + +
114B LEU 3.2 0.2 - - - -
115B GLY* 1.3 74.1 - - - +
117B GLN* 1.3 64.7 + - - +
119B LEU* 3.0 19.5 + - + +
120B LEU* 3.0 17.2 + - + +
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Residues in contact with GLN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.3 30.3 - - + -
45B ILE* 3.6 10.7 - - + +
46B PRO* 2.8 32.3 + - - +
47B GLY 4.3 0.2 - - - -
48B LYS* 4.0 38.2 - - + +
113B LEU 3.0 14.4 + - - +
114B LEU* 3.5 15.1 - - - +
116B ILE* 1.3 76.0 - - - +
118B GLU* 1.3 63.2 + - - +
120B LEU* 3.2 29.0 + - + +
121B ASN* 4.1 2.3 + - - +
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LYS* 5.1 14.6 + - - +
114B LEU 2.9 12.9 + - - +
115B GLY* 3.4 16.1 - - - +
117B GLN* 1.3 78.1 + - - +
119B LEU* 1.3 62.7 + - - +
120B LEU 3.2 0.5 + - - -
121B ASN* 3.6 2.6 + - - +
122B GLU* 3.3 47.1 + - + +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B HIS* 2.9 23.4 + - + +
85B ASN* 3.3 39.0 - - + +
86B VAL* 5.9 1.1 - - + -
92B VAL* 4.0 21.8 - - + -
93B CYS 4.1 2.7 - - - +
94B LEU* 3.7 28.9 - - + -
115B GLY 2.9 14.1 + - - +
116B ILE* 3.0 14.5 + - + +
118B GLU* 1.3 75.3 - - - +
120B LEU* 1.3 64.6 + - - +
122B GLU 3.3 29.0 + - - +
124B ASN* 4.0 11.0 - - + +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 4.1 17.0 - - + -
46B PRO 4.6 3.4 - - - +
47B GLY* 4.7 4.7 - - - -
48B LYS 5.6 0.7 - - - +
53B TRP* 2.9 58.3 + - + -
58B PHE* 4.4 14.4 - - + -
77B PHE* 4.5 14.4 - - + -
81B LEU* 4.5 13.2 - - + -
83B HIS* 3.0 24.6 + - + -
116B ILE* 3.0 18.1 + - + +
117B GLN* 3.2 24.9 - - + +
118B GLU 3.1 0.8 - - - -
119B LEU* 1.3 77.1 - - - +
121B ASN* 1.3 59.6 + - + +
123B PRO* 4.4 2.1 - - - +
144B TYR* 4.5 1.4 + - - -
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Residues in contact with ASN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LYS* 5.5 11.3 - - + +
50B GLY 5.3 0.2 + - - -
51B THR* 3.3 36.0 - - + +
52B PRO* 3.9 11.4 - - - +
53B TRP* 3.7 17.7 + - + +
117B GLN 4.1 2.6 + - - +
118B GLU 3.6 4.8 + - - +
120B LEU* 1.3 76.5 - - + +
122B GLU* 1.3 65.5 + - + +
123B PRO* 3.4 11.1 - - - +
137B TYR* 5.3 0.7 + - - -
144B TYR* 6.0 1.4 - - - -
145B GLU* 5.1 2.6 - - - +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LYS* 4.7 10.7 + - - +
118B GLU* 3.3 39.8 + - + +
119B LEU* 3.3 19.4 + - - +
121B ASN* 1.3 86.2 - - + +
123B PRO* 1.3 68.5 - - - +
124B ASN* 5.1 0.2 - - - +
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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