Contacts of the strand formed by residues 125 - 131 (chain A) in PDB entry 1YH7
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 PHE 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A LEU* 6.0 1.1 - - + -
66A SER 3.3 9.2 - - - +
68A ARG* 3.8 7.2 - - - -
72A LEU 3.8 5.7 + - - +
73A VAL* 3.3 21.8 - - + +
74A SER 3.1 21.0 + - - -
75A LEU* 3.9 5.6 - - + -
110A VAL* 3.2 34.3 - - + -
114A ILE* 3.6 23.6 - - + -
123A PRO* 4.0 14.1 - - + -
124A GLY* 1.4 77.4 - - - +
126A SER* 1.4 60.5 + - - +
127A ALA* 3.7 28.7 - - + -
149A THR* 5.8 2.7 - - + -
152A PHE* 3.6 24.9 - + + -
153A LEU* 4.1 26.0 - - + -
156A LEU* 3.9 5.4 - - + -
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Residues in contact with SER 126 (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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20A PHE* 3.4 24.3 - - - -
24A PHE* 4.5 16.8 - - - -
65A GLY* 3.0 4.5 - - - -
66A SER* 2.6 45.9 + - - +
67A PRO 5.2 0.6 + - - -
68A ARG* 3.8 15.7 - - - +
74A SER 3.5 6.5 - - - +
125A PHE* 1.4 76.4 - - - +
127A ALA* 1.4 61.0 + - - +
152A PHE* 3.9 3.5 - - - -
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Residues in contact with ALA 127 (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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24A PHE* 4.1 0.9 - - - -
63A LEU* 3.5 20.4 - - + -
64A VAL 3.6 4.3 - - - -
74A SER 2.7 11.1 + - - +
75A LEU* 3.1 24.7 - - + +
76A LEU 2.8 24.3 + - - +
110A VAL* 6.3 0.7 - - + -
125A PHE* 3.7 14.8 - - + -
126A SER* 1.4 78.2 - - - +
128A VAL* 1.3 64.9 + - - +
129A VAL* 5.0 2.7 - - + -
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Residues in contact with VAL 128 (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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16A ALA* 5.2 4.3 - - + +
19A ALA* 5.9 2.2 - - + -
20A PHE* 3.0 40.8 - - + +
23A GLU* 5.1 2.5 - - + -
24A PHE* 3.5 20.0 - - + -
63A LEU* 2.7 14.6 - - - +
64A VAL* 2.7 64.6 + - + +
76A LEU* 3.2 17.3 - - + +
127A ALA* 1.3 72.7 - - - +
129A VAL* 1.3 62.8 + - - +
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Residues in contact with VAL 129 (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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61A THR* 5.8 3.1 - - - -
62A VAL 3.2 7.6 - - - +
63A LEU* 2.9 40.2 - - + -
76A LEU 3.0 9.4 + - - +
77A THR* 3.8 19.9 + - - +
78A THR* 3.0 25.5 + - - -
106A TRP* 6.3 2.7 - - + -
127A ALA* 5.0 3.1 - - + -
128A VAL* 1.3 72.6 - - - +
130A VAL* 1.4 69.7 + - - +
131A SER* 6.3 1.1 - - - -
145A LEU* 4.6 23.1 - - + -
148A ALA* 5.8 1.6 - - + -
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Residues in contact with VAL 130 (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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11A GLU* 4.4 27.8 - - + +
16A ALA* 5.2 13.2 - - + -
60A MET 4.3 0.3 - - - +
61A THR* 3.3 1.0 - - - -
62A VAL* 2.6 53.1 + - + +
77A THR* 5.4 0.2 - - - -
78A THR* 2.9 37.7 - - + +
79A SER* 4.6 1.6 - - - +
129A VAL* 1.4 77.2 - - - +
131A SER* 1.4 67.6 + - - +
132A SER* 5.0 0.7 - - - +
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Residues in contact with SER 131 (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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60A MET 3.4 3.4 - - - -
61A THR* 2.9 31.4 - - - -
79A SER* 3.7 20.8 + - - -
129A VAL* 6.3 1.6 - - - -
130A VAL* 1.4 82.3 - - - +
132A SER* 1.3 62.0 + - - +
133A VAL* 3.4 18.9 + - - +
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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