Contacts of the strand formed by residues 109 - 114 (chain H) in PDB entry 5D7I
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 109 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H GLN* 2.9 23.3 + - - +
7H ALA 4.6 1.2 + - - -
8H PRO 2.7 26.7 + - - -
9H THR* 3.4 4.7 - - - -
21H LEU* 4.3 23.7 - - - +
34H TRP* 4.9 1.0 - - - -
87H SER 3.7 0.2 - - - +
88H VAL* 3.5 4.9 - - - +
89H TYR* 2.8 40.6 + - - +
108H GLY* 1.3 71.1 - - - -
110H ARG* 1.3 62.6 + - - +
111H LEU* 3.4 4.4 + - - -
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Residues in contact with ARG 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G GLY* 5.2 12.1 - - - -
9H THR 2.8 15.7 + - - +
10H SER* 3.4 2.4 - - - -
11H GLN 3.0 26.7 + - - +
87H SER 3.8 4.7 - - - +
88H VAL* 3.9 29.4 - - + +
108H GLY 4.2 0.6 + - - -
109H SER* 1.3 70.3 - - - +
111H LEU* 1.3 59.3 + - - +
112H THR* 4.1 11.3 + - - +
152H PRO* 6.4 0.9 - - - -
153H ASP* 4.2 21.1 + - - -
154H HIS* 3.6 53.7 + - + +
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Residues in contact with LEU 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H GLN* 3.5 35.9 - - + +
13H LEU* 4.3 15.5 - - + -
19H MET* 4.4 13.5 - - + -
21H LEU* 5.4 9.0 - - + -
78H LEU* 3.7 31.9 - - + -
85H GLN 3.7 15.3 - - - +
86H THR* 3.3 6.2 - - - +
87H SER 2.9 33.9 + - - +
89H TYR* 3.8 22.0 - - + -
109H SER* 3.4 1.9 + - - +
110H ARG* 1.3 74.3 - - - +
112H THR* 1.3 63.0 - - - +
113H VAL* 3.8 12.3 - - + -
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Residues in contact with THR 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H GLN 3.0 11.4 + - - +
12H ILE* 3.3 13.1 - - - +
13H LEU* 2.8 28.2 + - - +
86H THR* 3.9 14.8 - - + +
110H ARG* 4.9 11.3 + - - +
111H LEU* 1.3 74.9 + - - +
113H VAL* 1.3 63.4 + - - +
114H LEU* 3.7 30.1 - - + -
151H TYR* 5.1 1.8 - - - +
152H PRO* 3.8 30.4 - - + +
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Residues in contact with VAL 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H LEU* 3.3 12.1 - - + +
14H ALA 4.3 0.4 - - - +
15H ALA* 3.8 20.6 - - + -
81H ALA* 4.0 15.5 - - + -
82H VAL 3.5 39.7 - - - +
83H PRO* 3.5 16.9 - - - +
85H GLN* 4.1 1.8 - - + -
86H THR* 2.9 27.0 + - - +
111H LEU* 3.8 27.4 - - + -
112H THR* 1.3 76.9 - - - +
114H LEU* 1.3 65.3 + - - +
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Residues in contact with LEU 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ILE* 3.8 16.2 - - + -
13H LEU 2.9 8.3 + - - +
14H ALA* 3.4 6.9 - - - +
15H ALA* 2.9 22.7 + - - -
83H PRO* 5.0 0.7 - - - -
112H THR* 3.7 22.0 - - + -
113H VAL* 1.3 77.5 - - - +
115H GLU* 1.3 64.5 + - - +
116H ASP 3.6 22.7 - - - +
117H LEU* 4.2 4.4 - - + +
119H ASN* 6.0 0.7 - - + -
120H VAL* 3.6 31.9 - - + +
151H TYR* 3.6 36.6 - - + +
152H PRO* 5.3 0.9 - - + -
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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