Contacts of the strand formed by residues 81 - 86 (chain G) in PDB entry 1IB1
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 SER 81 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G CYS* 3.7 15.0 - - - -
40G LEU* 3.1 20.9 + - - -
74G LEU* 3.4 27.5 - - - +
77G CYS 4.8 0.9 - - - -
78G PRO* 2.7 24.1 + - - +
80G LEU* 1.3 80.2 - - - +
82G LEU* 1.3 66.3 + - - +
94G ILE 3.3 13.2 - - - -
95G ILE* 4.4 6.3 - - - -
96G GLY 4.6 0.7 - - - -
143G TYR* 4.1 2.7 - - - -
146G HIS* 4.2 4.9 + - - -
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Residues in contact with LEU 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G PHE* 4.2 11.7 - - + -
38G ARG* 3.2 34.1 - - - +
39G CYS* 4.2 1.8 - - - +
40G LEU* 4.2 5.8 - - - +
81G SER* 1.3 79.7 - - - +
83G GLY* 1.3 59.3 + - - +
93G PHE* 3.4 2.4 - - - +
94G ILE 3.0 31.4 + - - -
139G LEU* 3.8 20.5 - - + +
142G ARG* 3.9 18.8 - - + +
143G TYR* 3.8 43.7 - - + +
146G HIS* 4.6 19.3 - - + +
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Residues in contact with GLY 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G PHE* 3.4 9.8 - - - -
38G ARG 2.9 32.3 + - - -
40G LEU* 3.8 17.9 - - - +
82G LEU* 1.3 76.4 - - - +
84G TRP* 1.3 60.8 + - - -
85G PHE* 3.3 8.8 - - - -
90G LEU* 4.0 0.9 - - - -
92G ALA 3.2 11.2 - - - -
93G PHE* 4.2 0.4 - - - -
139G LEU* 4.5 1.6 - - - -
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Residues in contact with TRP 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU* 4.5 13.2 - - - -
15C GLN* 6.5 1.1 - - + -
35G ASN* 3.5 30.2 - - + +
36G GLU 3.6 7.0 - - - -
37G PHE* 3.3 35.2 - + + -
83G GLY* 1.3 70.5 - - - -
85G PHE* 1.3 66.1 + - - +
86G VAL* 3.3 30.9 - - + +
90G LEU* 3.8 2.3 - - - +
91G VAL* 3.1 30.9 + - + +
92G ALA* 2.9 25.2 + - + -
135G LYS* 3.7 55.6 - - + -
138G VAL* 3.4 37.5 - - + -
139G LEU* 4.5 5.1 - - + +
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Residues in contact with PHE 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C ASP 5.5 0.7 - - - -
216C LEU* 4.0 29.4 - - + -
35G ASN* 3.2 5.0 + - - -
36G GLU* 2.9 43.9 + - + +
38G ARG* 3.6 36.3 - - + -
39G CYS 5.0 2.0 - - - -
40G LEU* 3.5 31.4 - - + -
44G ASP* 4.0 20.0 - - - -
83G GLY 3.3 18.8 - - - -
84G TRP* 1.3 73.5 - - - +
86G VAL* 1.3 61.1 + - - +
87G GLU 3.2 2.6 + - - -
88G GLY 4.2 6.2 + - - +
89G ARG 3.1 6.5 - - - +
90G LEU* 3.6 32.3 - - + -
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Residues in contact with VAL 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ASN* 3.2 36.1 - - + +
35G ASN* 3.6 6.5 - - - +
84G TRP* 3.3 27.7 + - + +
85G PHE* 1.3 67.7 - - - +
87G GLU* 1.3 71.7 + - + +
89G ARG* 2.7 30.0 + - + +
91G VAL* 3.7 23.1 - - + -
130G PHE* 4.6 17.7 - - + -
135G LYS* 6.4 0.7 - - + -
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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