Contacts of the strand formed by residues 105 - 116 (chain T) in PDB entry 5IYB
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 105 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7T LEU* 3.8 6.1 - - - -
8T ASP* 3.3 26.4 + - - +
96T PHE* 3.1 1.9 - - - -
97T THR* 2.6 49.8 + - - -
103T LYS* 3.6 8.3 + - - +
104T LEU* 1.3 79.2 + - - +
106T LEU* 1.3 61.5 + - - +
107T GLU* 3.6 9.7 + - - -
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Residues in contact with LEU 106 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29S MET* 3.9 10.8 - - + -
39S PHE* 6.0 0.9 - - + -
42S TRP* 4.4 18.6 - - + -
7T LEU* 3.8 7.9 - - + +
8T ASP* 2.8 22.4 + - - +
9T LEU* 3.7 18.8 - - + -
10T THR* 4.9 1.0 + - - -
11T GLY* 3.3 21.3 + - - -
12T ALA* 3.6 27.1 - - + -
94T THR* 3.8 25.1 - - + +
95T VAL 3.3 23.6 - - - +
96T PHE* 3.8 11.0 - - + -
105T SER* 1.3 72.1 - - - +
107T GLU* 1.3 64.3 + - - +
108T GLY 4.7 4.5 - - - +
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Residues in contact with GLU 107 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24S LYS* 2.7 31.9 + - - -
26S TYR* 5.0 4.3 - - + -
11T GLY* 3.5 10.6 - - - -
16T THR* 3.4 20.3 + - - +
18T VAL* 6.1 3.1 - - + -
95T VAL* 2.6 25.2 + - + +
97T THR* 3.3 33.6 + - + +
105T SER* 4.3 9.1 - - - +
106T LEU* 1.3 73.3 - - - +
108T GLY* 1.3 55.6 + - - +
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Residues in contact with GLY 108 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11T GLY 4.3 7.9 - - - -
12T ALA* 4.7 1.5 - - - +
16T THR* 3.3 17.5 - - - -
18T VAL* 5.0 8.3 - - - -
94T THR* 3.1 6.9 - - - -
95T VAL* 2.8 25.6 + - - +
106T LEU* 3.5 4.3 - - - +
107T GLU* 1.3 82.0 - - - +
109T ILE* 1.3 64.7 + - - -
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Residues in contact with ILE 109 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39S PHE* 3.8 25.6 - - + -
12T ALA* 4.0 19.5 - - + +
15T ASN* 3.9 32.8 - - - +
16T THR 2.5 23.9 + - - +
17T GLY* 3.2 8.0 - - - -
18T VAL* 3.0 24.6 + - - -
92T THR* 4.8 6.3 - - + -
93T LEU 3.2 10.8 - - - +
94T THR* 3.6 19.5 - - + -
108T GLY* 1.3 75.3 - - - -
110T VAL* 1.3 74.0 + - - +
111T VAL* 3.3 7.7 + - + +
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Residues in contact with VAL 110 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28S ILE* 4.6 4.5 - - + -
126S ILE* 5.2 1.6 - - + -
18T VAL* 3.6 22.0 - - + +
20T LEU* 4.0 17.0 - - + -
88T VAL* 5.0 9.2 - - + +
92T THR* 5.9 0.2 - - - +
93T LEU* 2.5 57.3 + - + +
94T THR* 4.1 9.9 - - - +
95T VAL* 4.5 7.4 - - + -
109T ILE* 1.3 76.0 - - - +
111T VAL* 1.3 61.4 + - - +
112T GLN 3.5 24.7 - - - +
113T ARG* 4.8 5.2 - - + -
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Residues in contact with VAL 111 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15T ASN* 5.7 2.2 - - - +
17T GLY* 3.7 15.3 - - - -
18T VAL 3.0 19.6 + - - +
19T TRP* 3.8 18.6 - - + +
88T VAL* 3.8 19.1 - - - +
109T ILE* 3.7 19.3 - - + +
110T VAL* 1.3 74.7 - - - +
112T GLN* 1.3 67.9 + - + +
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Residues in contact with GLN 112 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18T VAL 3.6 0.8 + - - -
19T TRP* 3.5 40.3 - - + +
20T LEU 2.7 31.2 + - - -
85T LEU* 4.0 33.5 - - + +
86T GLN 3.3 14.2 + - - +
88T VAL* 3.9 9.1 - - - +
110T VAL* 3.5 7.9 - - - +
111T VAL* 1.3 85.7 + - - +
113T ARG* 1.3 82.9 + - - +
114T ALA* 5.4 0.9 - - + -
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Residues in contact with ARG 113 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551B GLU* 4.7 12.5 + - - +
555B GLU* 3.2 41.4 + - - +
556B ILE* 5.6 0.6 - - - +
143S TRP* 5.0 9.1 - - - -
20T LEU* 3.3 28.7 - - + +
22T LYS* 6.1 0.4 - - - +
85T LEU* 3.3 2.8 - - - -
86T GLN* 2.8 51.4 + - + +
87T SER 3.8 17.3 + - - -
88T VAL* 3.5 15.0 - - + +
91T GLN* 4.3 16.2 + - - +
93T LEU* 5.4 8.6 - - + +
110T VAL* 4.8 3.8 - - + -
112T GLN* 1.3 87.6 + - - +
114T ALA* 1.3 66.6 + - - +
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Residues in contact with ALA 114 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19T TRP* 6.2 3.6 - - + -
20T LEU 2.7 13.0 + - - +
21T VAL* 3.2 20.5 - - + -
22T LYS* 2.8 24.7 + - - +
83T PHE* 4.3 12.1 - - + -
84T VAL 3.1 13.7 - - - +
85T LEU* 3.8 17.0 - - + -
86T GLN* 4.3 4.9 - - - +
112T GLN* 5.4 1.1 - - + -
113T ARG* 1.3 77.7 - - - +
115T GLU* 1.3 61.7 + - - +
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Residues in contact with GLU 115 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546B GLU 4.7 4.2 - - - +
547B GLU 4.1 16.1 - - - +
548B TRP 4.2 6.6 - - - +
549B SER* 4.4 17.0 - - - +
551B GLU* 6.0 1.4 - - - +
21T VAL* 4.5 1.1 - - - -
22T LYS* 3.5 36.0 + - + +
82T PRO 3.7 0.2 - - - +
83T PHE* 3.6 2.5 - - - -
84T VAL* 2.8 54.8 + - + +
86T GLN* 4.4 12.8 + - + +
114T ALA* 1.3 74.8 - - - +
116T CYS* 1.3 72.5 + - - +
117T ARG* 3.5 13.0 + - + +
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Residues in contact with CYS 116 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21T VAL* 4.1 2.5 - - + +
22T LYS 2.5 19.1 + - - +
23T VAL* 3.7 14.6 - - + -
24T PRO* 3.1 29.0 - - + +
27T LEU* 4.2 10.8 - - - -
81T HIS* 3.3 46.4 - - - -
82T PRO 3.7 4.3 - - - -
83T PHE* 3.9 18.8 - - + -
115T GLU* 1.3 76.4 - - - +
117T ARG* 1.3 59.2 + - - +
118T PRO* 4.5 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