Contacts of the strand formed by residues 107 - 115 (chain B) in PDB entry 1TDR
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 ALA 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B ILE* 3.5 13.2 - - - +
4B LEU* 4.3 14.1 - - + -
103B PHE 3.0 7.1 + - - +
104B LEU* 2.7 39.9 + - + +
106B LYS* 1.3 70.4 - - - +
108B GLN* 1.3 60.8 - - - +
109B LYS 4.5 6.7 - - - +
110B LEU* 4.7 2.5 - - + -
133B TRP* 3.6 9.2 - - + -
158B ARG* 2.5 34.3 + - - -
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Residues in contact with GLN 108 (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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1B MET* 3.9 26.2 - - + -
2B ILE 3.1 7.2 + - - +
105B PRO 4.3 2.4 + - - -
106B LYS* 2.7 31.3 + - - +
107B ALA* 1.3 77.0 + - - +
109B LYS* 1.3 57.9 + - - +
133B TRP* 3.7 2.9 - - - -
157B GLU* 3.4 3.8 - - - +
158B ARG* 2.5 65.4 + - + +
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Residues in contact with LYS 109 (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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1B MET* 4.4 15.5 - - - +
2B ILE 4.0 1.6 + - - +
3B SER* 3.3 20.0 - - - +
4B LEU 3.1 22.7 + - - -
90B GLU* 4.3 4.6 + - - +
107B ALA* 3.6 1.8 - - - +
108B GLN* 1.3 80.7 - - - +
110B LEU* 1.3 63.4 + - - +
111B TYR* 3.5 30.0 + - + +
133B TRP* 3.7 2.0 - - - -
136B VAL* 5.6 0.2 - - - -
155B ILE* 3.5 27.5 - - + +
156B LEU 3.0 20.9 - - - +
157B GLU* 3.9 21.7 + - + -
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Residues in contact with LEU 110 (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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4B LEU* 3.4 22.0 - - + -
104B LEU* 4.5 12.1 - - + -
107B ALA* 4.7 1.6 - - + -
109B LYS* 1.3 77.3 - - - +
111B TYR* 1.3 63.6 + - - +
112B LEU* 4.0 17.0 - - + -
125B PHE* 4.5 10.3 - - + -
128B TYR* 3.8 40.8 - - + -
133B TRP* 3.7 30.7 - - + -
154B LYS 3.5 0.5 - - - +
155B ILE* 3.2 7.3 - - - +
156B LEU* 2.9 48.2 + - + +
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Residues in contact with TYR 111 (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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3B SER* 3.9 8.1 - - - -
4B LEU 2.9 15.8 + - - -
5B ILE* 3.2 20.6 - - + +
6B ALA 3.0 24.8 + - - +
30B TRP* 4.2 9.0 - + + +
34B ASN* 3.2 41.3 - - + -
38B LYS* 4.6 2.3 + - - -
90B GLU* 2.9 33.9 + - - -
92B MET* 3.8 19.5 - - + -
109B LYS* 3.5 29.0 + - + -
110B LEU* 1.3 75.7 - - - +
112B LEU* 1.3 61.5 + - - +
154B LYS 3.3 5.6 - - - -
155B ILE* 3.9 24.9 - - + -
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Residues in contact with LEU 112 (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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4B LEU 5.2 0.9 - - - +
6B ALA* 3.5 22.2 - - + +
8B LEU* 4.3 10.5 - - + -
30B TRP* 4.6 2.7 - - - -
110B LEU* 4.1 21.3 - - + -
111B TYR* 1.3 87.8 - - - +
113B THR* 1.3 66.0 + - - +
114B HIS* 3.9 25.8 - - + +
125B PHE* 4.2 15.9 - - + -
128B TYR* 3.5 34.8 - - + +
152B CYS 3.5 0.7 - - - +
153B PHE* 3.2 4.5 - - - -
154B LYS* 2.6 50.3 + - + +
156B LEU* 4.8 2.5 - - + -
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Residues in contact with THR 113 (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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6B ALA 2.9 10.3 + - - -
7B ALA* 3.4 4.4 - - - -
8B LEU* 2.6 35.8 + - - +
27B ASP* 2.8 35.4 + - + +
30B TRP* 3.7 8.3 + - - -
112B LEU* 1.3 74.0 - - - +
114B HIS* 1.3 60.5 - - - +
115B ILE* 3.7 7.1 + - + +
151B TYR* 3.8 22.9 - - + -
152B CYS 3.3 2.0 - - - +
153B PHE* 3.6 30.6 - - + -
170B MTX 3.7 3.1 + - - -
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Residues in contact with HIS 114 (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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8B LEU* 3.6 20.9 + - + +
112B LEU* 3.9 24.3 - - + +
113B THR* 1.3 71.3 - - - +
115B ILE* 1.3 61.4 + - - +
128B TYR* 4.1 9.4 - - - -
151B TYR* 3.0 5.4 - - - -
152B CYS* 2.7 55.2 + - + +
154B LYS* 2.9 45.4 - - + +
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Residues in contact with ILE 115 (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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7B ALA* 3.5 34.8 - - + -
8B LEU 2.9 11.8 + - - +
9B ALA* 3.6 4.4 - - - -
10B VAL* 3.6 20.3 + - - +
22B TRP* 3.8 26.7 - - + +
24B LEU* 3.4 34.1 - - + -
27B ASP* 5.1 1.1 - - - -
113B THR* 4.2 11.2 - - + +
114B HIS* 1.3 77.5 - - - +
116B ASP* 1.3 61.5 + - - +
117B ALA* 3.1 23.2 + - + -
149B HIS* 3.8 24.5 - - + -
150B SER 3.7 4.5 - - - +
151B TYR* 4.3 1.1 - - + +
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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