Contacts of the strand formed by residues 66 - 73 (chain B) in PDB entry 1IJK
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 TYR 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B ASP* 3.6 1.5 - - - +
65B LEU* 1.3 116.1 - - + +
67B ALA* 1.3 61.5 + - - +
68B TRP 4.2 0.7 - - - -
105B ALA* 3.9 11.4 - - + -
106B LEU 3.2 11.2 - - - +
107B GLU* 4.2 11.9 - - + -
112B PHE* 4.3 4.0 - - - -
116B ILE* 4.1 34.1 - - + +
118B LEU* 3.7 23.8 - - + +
122B GLN* 3.5 26.0 - - - -
124B ASN* 3.7 13.9 + - - +
125B PRO* 3.1 30.1 - - - +
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Residues in contact with ALA 67 (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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16B PHE* 4.5 11.4 - - + -
56B VAL* 4.2 30.3 - - + -
60B ILE* 5.6 0.2 - - + -
66B TYR* 1.3 75.3 - - - +
68B TRP* 1.3 67.7 + - - +
69B ILE* 3.8 0.9 - - - +
105B ALA* 3.6 2.2 - - - -
106B LEU* 2.6 47.6 + - + +
112B PHE* 4.5 1.8 - - + -
125B PRO* 3.4 10.1 - - + +
126B PHE* 4.6 2.7 - - - -
127B VAL* 4.7 3.1 - - + -
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Residues in contact with TRP 68 (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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21B MET 2.9 27.7 + - - -
22B ASN 3.3 0.6 - - - -
23B TRP* 3.0 28.8 - + + +
26B ALA* 4.1 7.6 - - + -
39B LEU* 3.9 15.1 - - + +
40B VAL* 4.3 0.7 - - - +
66B TYR 4.2 0.6 - - - -
67B ALA* 1.3 74.7 - - - +
69B ILE* 1.3 63.7 + - - +
103B CYS* 3.2 38.1 - - + -
104B PHE 3.1 24.7 - - - -
105B ALA* 3.7 5.5 - - + +
118B LEU* 3.9 19.3 - - + -
119B TYR 3.8 16.2 - - - -
120B CYS* 3.7 11.2 - - - -
122B GLN 3.4 13.4 + - - -
124B ASN* 3.2 37.7 - - + +
125B PRO 3.1 8.0 + - - -
126B PHE* 3.9 10.5 - - + -
127B VAL* 3.6 20.6 + - - +
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Residues in contact with ILE 69 (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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23B TRP* 2.9 23.7 + - - -
39B LEU* 3.4 7.5 - - - +
40B VAL* 3.8 21.5 - - + +
42B ILE* 4.4 4.7 - - + -
67B ALA 3.8 2.0 - - - +
68B TRP* 1.3 79.5 - - - +
70B GLY* 1.3 59.8 + - - +
71B LEU* 3.3 4.6 + - + +
104B PHE* 3.0 38.9 + - + +
105B ALA 4.6 2.2 - - - +
106B LEU* 3.5 35.0 - - + +
115B TRP* 4.1 28.3 - - + +
279C TRP* 3.9 24.2 - - + -
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Residues in contact with GLY 70 (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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23B TRP* 3.6 7.8 - - - -
39B LEU* 3.3 24.6 - - - +
40B VAL 2.7 21.3 + - - -
69B ILE* 1.3 70.1 - - - +
71B LEU* 1.3 60.4 + - - +
72B ARG* 3.7 1.0 + - - +
278C GLU 3.7 0.5 - - - +
279C TRP* 3.5 8.5 - - - -
280C THR* 2.9 33.4 + - - -
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Residues in contact with LEU 71 (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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23B TRP* 3.8 4.2 + - - -
69B ILE* 3.3 3.2 - - + -
70B GLY* 1.3 78.6 - - - +
72B ARG* 1.3 67.1 + - - +
104B PHE* 3.0 55.3 + - + +
115B TRP* 3.4 38.8 - - + -
277C PHE* 3.5 27.8 - - + -
278C GLU 3.6 16.2 - - - +
279C TRP* 3.4 32.7 - - + +
290C TYR* 4.1 10.8 - - + -
293C ILE* 4.9 1.6 - - + -
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Residues in contact with ARG 72 (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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23B TRP* 3.2 48.2 - - + -
24B ALA* 6.0 1.4 - - - +
70B GLY 5.1 0.2 - - - +
71B LEU* 1.3 77.0 - - - +
73B VAL* 1.3 77.5 + - - +
74B GLU 3.2 2.6 + - - -
102B LYS* 3.2 30.1 + - - +
103B CYS* 4.3 3.5 - - - -
104B PHE* 4.3 2.0 - - - -
120B CYS* 3.9 21.2 - - - +
277C PHE* 3.6 7.0 - - - -
278C GLU* 3.3 43.9 + - + +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ARG* 1.3 90.0 + - - +
74B GLU* 1.3 63.4 + - - +
75B ASN 3.7 11.4 - - - +
80B CYS* 3.8 21.8 - - - -
101B LYS 4.3 5.4 - - - +
102B LYS* 2.7 61.4 + - + +
104B PHE* 4.6 6.0 - - + -
117B ASN* 5.7 0.2 - - + -
272C TRP* 4.4 5.2 - - + +
275C CYS* 3.8 18.2 - - + -
276C ARG 3.5 4.5 - - - -
277C PHE* 3.9 17.0 - - + -
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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