Contacts of the strand formed by residues 107 - 115 (chain F) in PDB entry 2Y1T
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 ARG 107 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B THR 4.5 7.1 + - - -
13B THR* 5.2 3.6 + - - +
27B ARG* 5.2 0.6 - - - +
104B LYS* 3.3 59.8 + - - +
105B GLY* 4.6 7.1 - - - -
16F ASN* 4.6 10.7 + - - +
25F ASP* 3.1 30.4 + - + +
26F LEU 3.4 8.5 - - - +
27F ARG* 3.4 48.3 - - + +
61F ARG* 3.1 39.6 + - - +
64F THR* 4.9 0.7 + - - -
68F PHE* 3.9 13.7 - - - -
105F GLY 3.3 2.6 + - - +
106F ASP* 1.3 70.2 - - - +
108F ILE* 1.3 59.7 + - - +
109F CYS 3.8 0.2 - - - -
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Residues in contact with ILE 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F LEU 2.9 9.4 + - - +
28F ALA* 4.2 4.5 - - + +
42F VAL* 3.2 35.0 - - + -
44F LEU* 3.4 26.7 - - + -
61F ARG* 4.0 2.4 + - - -
64F THR* 3.0 33.3 + - + +
68F PHE* 4.5 9.6 - - + -
92F PHE* 3.8 26.6 - - + -
102F ILE* 3.9 29.6 - - + -
106F ASP* 3.3 15.7 + - + +
107F ARG* 1.3 76.4 - - - +
109F CYS* 1.3 67.8 + - - +
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Residues in contact with CYS 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F ASP* 3.5 0.2 - - - -
26F LEU* 2.8 32.8 + - - -
44F LEU* 3.7 30.5 - - - -
58F VAL* 3.6 24.5 - - + -
59F VAL 3.9 10.5 - - - +
61F ARG* 3.3 20.0 - - - +
92F PHE* 3.5 27.1 - - + -
108F ILE* 1.3 79.7 - - - +
110F GLN* 1.3 61.2 + - - +
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Residues in contact with GLN 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D VAL* 3.9 21.2 - - - +
143D DUD 4.8 11.9 + - - -
23F TRP* 3.5 40.5 - - + +
24F ILE 3.2 13.2 - - - +
25F ASP* 3.8 13.2 - - - +
26F LEU* 4.4 2.0 - - - +
57F HIS 3.8 0.5 - - - +
58F VAL* 3.2 6.7 - - - -
59F VAL* 3.0 41.6 + - + +
60F PRO 3.9 8.7 - - - +
61F ARG* 3.7 18.7 + - + +
62F SER 4.8 0.8 + - - -
109F CYS* 1.3 78.2 - - - +
111F PHE* 1.3 62.1 + - - +
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Residues in contact with PHE 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D MET* 4.2 1.9 - - - +
122D LEU* 5.1 3.4 - - + -
3F ILE* 4.2 20.0 - - + -
15F ILE* 4.9 2.5 - - + -
23F TRP* 3.3 9.0 - - - -
24F ILE* 2.7 81.7 + - + +
26F LEU* 3.7 28.5 - - + -
48F MET* 3.7 24.5 - - + -
50F LEU* 4.9 0.4 - - + -
56F ALA* 3.9 11.0 - - + -
57F HIS 3.2 13.2 - - - +
58F VAL* 4.0 15.7 - - + -
90F TRP* 3.9 10.8 - + + -
110F GLN* 1.3 76.3 - - - +
112F ARG* 1.3 74.2 + - - +
113F ILE* 4.3 9.6 - - + -
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Residues in contact with ARG 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D GLU* 2.9 22.0 + - - -
57D HIS* 5.1 0.4 - - - -
114D MET* 4.1 9.8 - - - -
115D LYS* 2.9 29.1 + - - +
116D LYS* 3.8 3.0 + - - +
117D MET* 3.5 38.4 - - + +
118D PRO* 5.2 1.2 - - - +
23F TRP* 3.5 45.9 - - + +
56F ALA* 3.2 4.5 - - - +
57F HIS* 2.9 36.1 + - + +
111F PHE* 1.3 81.0 - - - +
113F ILE* 1.3 86.1 + - - +
114F MET* 4.1 29.0 - - + +
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Residues in contact with ILE 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D MET* 3.5 23.6 - - + +
118D PRO* 4.9 2.3 - - + +
120D VAL* 4.6 14.4 - - + -
1F MET* 4.0 17.3 - - + -
3F ILE* 4.1 13.5 - - + -
50F LEU* 4.0 27.6 - - + -
51F PRO* 3.9 22.7 - - + -
54F TYR* 3.8 24.0 - - + -
55F GLU 3.1 11.7 - - - +
56F ALA* 4.5 1.8 - - + -
111F PHE* 4.3 5.6 - - + -
112F ARG* 1.3 103.2 + - - +
114F MET* 1.3 61.1 + - - +
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Residues in contact with MET 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D HIS* 5.0 4.5 - - + -
114D MET* 3.8 26.0 - - + +
118D PRO* 6.5 0.2 - - - -
112E ARG* 4.2 4.9 - - - +
114E MET* 3.2 33.7 - - + +
23F TRP* 6.0 0.2 - - + -
54F TYR* 3.2 8.2 - - - -
55F GLU* 2.8 33.2 + - - +
57F HIS* 3.1 40.8 - - + +
112F ARG* 4.1 25.4 - - - +
113F ILE* 1.3 71.8 - - - +
115F LYS* 1.3 72.1 + - + +
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Residues in contact with LYS 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E ARG* 2.9 22.6 + - - -
53F GLY* 3.6 26.8 + - - +
54F TYR* 3.3 31.1 - - + +
114F MET* 1.3 77.5 - - + +
116F LYS* 1.3 73.4 + - - +
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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