Contacts of the strand formed by residues 84 - 91 (chain L) in PDB entry 2IG2
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 84 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35L TYR 3.5 0.2 - - - +
36L GLN* 3.3 7.6 - - - +
37L GLN* 2.8 40.0 + - - +
39L PRO* 3.3 26.0 - - - +
83L THR* 1.3 77.9 - - - +
85L TYR* 1.3 62.8 + - - +
86L TYR* 3.7 31.6 + - + +
102L GLY* 6.1 0.2 - - - -
103L THR 3.3 5.4 - - - +
104L LYS* 2.7 49.0 + - - +
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Residues in contact with TYR 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L GLN* 3.0 16.3 + - - -
20L ILE* 3.7 19.5 - - + -
34L TRP* 4.6 5.2 - + + -
35L TYR 3.4 9.4 - - - +
36L GLN* 2.8 31.4 + - + -
46L LEU* 3.4 20.2 - - + -
61L PHE* 4.1 10.5 - + - -
72L LEU* 3.5 22.0 - - + -
74L ILE* 4.3 5.6 - - + -
81L ASP* 3.0 38.9 + - - +
83L THR* 3.1 24.1 + - - -
84L ASP* 1.3 70.9 - - - +
86L TYR* 1.3 57.1 - - - +
102L GLY* 3.5 0.3 - - - -
103L THR* 2.7 37.9 + - - +
105L VAL* 3.5 24.2 - - + -
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Residues in contact with TYR 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H GLN* 3.9 4.2 + - - -
43H LYS 4.2 2.8 + - - -
44H GLY* 3.8 14.1 - - - -
45H LEU* 3.7 36.8 - - + -
6L GLN* 3.4 2.7 - - - -
33L ASN 3.7 0.2 - - - +
34L TRP* 3.5 6.9 - - - -
35L TYR* 2.9 49.8 + - + +
37L GLN* 3.0 46.9 + - + -
84L ASP* 3.7 26.3 + - + +
85L TYR* 1.3 71.2 - - - +
87L CYS* 1.3 65.7 + - - +
99L PHE* 4.6 11.0 - + + -
100L GLY 4.1 12.8 - - - +
101L THR 4.8 0.2 - - - -
102L GLY* 3.8 24.9 - - - -
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Residues in contact with CYS 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L LEU* 4.2 13.7 - - - -
6L GLN* 3.0 18.2 + - - -
22L CYS* 2.1 51.8 - - - -
32L VAL* 3.8 6.7 - - + -
33L ASN 3.3 5.6 - - - -
34L TRP* 3.7 23.3 - - + -
86L TYR* 1.3 76.3 - - - +
88L ALA* 1.3 64.2 + - - +
99L PHE* 3.6 1.0 - - - -
100L GLY* 2.7 27.6 + - - -
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Residues in contact with ALA 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L LEU* 3.9 4.0 - - - -
31L THR 3.5 1.6 - - - +
32L VAL* 3.3 6.5 - - - +
33L ASN 3.0 28.9 + - - +
35L TYR* 4.3 5.2 - - + -
87L CYS* 1.3 79.4 - - - +
89L ALA* 1.3 63.5 + - - +
97L TYR* 3.6 27.7 + - + +
98L VAL 3.3 10.1 - - - +
99L PHE* 3.4 26.5 - - + -
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Residues in contact with ALA 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L LEU* 3.8 4.6 - - + +
27L ASN* 3.8 45.5 - - + +
30L SER 4.8 0.2 - - - +
31L THR 3.5 18.4 - - - +
32L VAL* 4.3 0.9 - - + -
88L ALA* 1.3 76.8 - - - +
90L TRP* 1.3 60.3 + - - +
91L ASP 3.1 9.4 + - - -
97L TYR* 4.3 4.6 - - - -
98L VAL* 2.9 33.2 + - - +
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Residues in contact with TRP 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H TRP* 4.4 0.4 - + - -
50H ILE* 3.8 39.7 - - + -
52H TRP* 4.1 10.5 - + - -
59H HIS* 4.5 4.9 - + - -
101H CYS* 3.8 30.5 - - - +
102H SER* 4.2 16.5 - - - +
103H SER 4.9 0.2 - - - +
104H CYS* 3.4 30.9 - - - +
27L ASN* 3.7 4.6 - - - +
30L SER* 3.3 24.8 - - - +
31L THR 4.6 1.0 + - - -
89L ALA* 1.3 67.1 - - - +
91L ASP* 1.3 58.0 + - - +
92L VAL* 3.1 35.9 + - + +
95L ASN* 3.7 37.1 + - + +
96L ALA* 3.6 10.1 - - - -
97L TYR* 3.5 39.9 - + + -
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Residues in contact with ASP 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1L GLN 5.2 1.9 - - - +
25L THR* 5.2 0.2 - - - +
27L SER* 2.8 49.9 + - - +
89L ALA 3.1 3.2 + - - -
90L TRP* 1.3 70.5 - - - +
92L VAL* 1.3 52.1 + - - +
93L SER* 2.8 39.5 + - - -
94L LEU* 3.4 21.7 + - + +
95L ASN* 2.7 36.9 + - - -
96L ALA 2.7 11.4 + - - +
98L VAL* 3.5 23.9 - - + +
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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