Contacts of the strand formed by residues 108 - 116 (chain A) in PDB entry 5YTX
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 THR 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LEU* 4.4 9.2 - - + -
61A GLY 3.4 13.3 + - - +
62A THR* 4.4 9.2 + - - +
78A ASN* 4.9 8.0 + - - +
106A GLY 3.7 3.1 + - - -
107A GLU* 1.3 80.3 - - - +
109A VAL* 1.3 73.4 + - - +
128A PRO* 3.3 37.6 - - + +
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A VAL 3.7 0.3 - - - +
60A LEU* 3.4 9.9 - - - +
61A GLY 2.9 35.5 + - - +
63A VAL* 4.1 11.4 - - + -
75A ILE* 3.9 32.5 - - + -
103A VAL* 4.1 20.0 - - + -
107A GLU* 4.0 23.3 - - + +
108A THR* 1.3 79.5 - - - +
110A GLU* 1.3 59.6 + - - +
111A PHE* 3.9 8.0 - - + -
125A VAL* 3.9 6.5 - - + -
126A THR 3.3 16.4 - - - +
128A PRO* 4.5 2.5 - - - -
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LYS* 3.5 40.0 - - - +
59A VAL 3.2 9.9 - - - +
60A LEU* 3.9 14.9 - - + +
109A VAL* 1.3 73.4 - - - +
111A PHE* 1.3 65.9 + - - +
124A ASN 3.6 1.4 - - - +
125A VAL* 3.5 0.7 - - - +
126A THR* 2.8 38.7 + - - +
127A GLY 3.7 13.2 - - - +
128A PRO* 3.7 1.9 - - + +
129A GLY* 2.8 32.7 + - - -
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Residues in contact with PHE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LYS* 3.4 3.0 + - - -
59A VAL* 2.8 63.1 + - + +
61A GLY 3.6 19.5 - - - -
75A ILE* 3.6 26.9 - - + -
77A ARG* 3.9 14.6 - - + -
84A VAL* 4.6 6.1 - - + -
109A VAL* 3.9 13.5 - - + -
110A GLU* 1.3 81.4 - - - +
112A ASP* 1.3 82.0 + - - +
113A VAL* 3.7 20.9 - - + -
122A ALA* 3.9 16.2 - - + -
123A ALA 3.5 12.3 - - - +
124A ASN 3.8 3.8 - - - -
125A VAL* 3.9 15.5 - - + -
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Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 4.7 3.6 - - + +
56A ALA 3.3 9.6 - - - +
57A THR* 3.3 32.8 - - + +
58A LYS* 3.3 6.8 + - - +
111A PHE* 1.3 78.2 - - - +
113A VAL* 1.3 61.6 + - - +
114A VAL* 4.6 7.4 - - + -
122A ALA* 3.3 5.4 - - - -
123A ALA* 2.8 40.4 + - + +
124A ASN* 2.8 32.6 + - - +
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL 3.8 0.2 - - - -
55A ILE* 2.8 40.6 + - + -
56A ALA* 2.9 21.0 + - + +
59A VAL* 4.0 14.4 - - + -
77A ARG* 4.0 28.7 - - - +
84A VAL* 4.7 7.6 - - + -
111A PHE* 3.7 27.8 - - + -
112A ASP* 1.3 73.9 - - - +
114A VAL* 1.3 59.9 + - - +
120A ALA* 3.9 25.8 - - + -
121A GLU 3.5 6.1 - - - +
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Residues in contact with VAL 114 (chain A).
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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52A LYS* 4.4 12.1 - - - +
53A LYS 3.2 10.8 - - - +
54A VAL* 4.1 23.1 - - + -
55A ILE* 4.6 3.8 - - - -
112A ASP* 4.6 5.4 - - + -
113A VAL* 1.3 79.5 - - - +
115A GLU* 1.3 64.1 + - - +
116A GLY* 3.4 0.7 + - - -
120A ALA* 3.2 5.5 - - - -
121A GLU* 2.8 62.1 + - + +
123A ALA* 3.8 27.4 - - + -
124A ASN* 6.1 0.2 - - - +
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LYS 3.1 23.7 + - - -
53A LYS* 2.8 30.9 + - + +
55A ILE* 4.5 14.8 - - + +
114A VAL* 1.3 71.9 - - - +
116A GLY* 1.3 65.5 - - - +
119A GLY* 4.0 18.0 - - - -
120A ALA* 3.6 17.2 + - - +
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Residues in contact with GLY 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LYS 5.2 0.7 - - - -
114A VAL* 3.4 4.0 + - - -
115A GLU* 1.3 84.3 - - - +
117A GLU* 1.3 66.0 + - - -
118A LYS 3.2 3.8 + - - -
119A GLY 2.7 21.1 + - - +
121A GLU* 3.2 27.0 + - - +
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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