Contacts of the strand formed by residues 46 - 55 (chain A) in PDB entry 5GQQ
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 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A PRO* 5.9 1.3 - - + -
24A GLY 6.3 0.4 - - - +
44A GLY 3.5 7.1 + - - +
45A PRO* 1.3 76.0 - - - +
47A LYS* 1.3 65.8 + - - +
48A TRP* 4.0 9.0 - - - +
110A TYR* 3.9 26.5 - - + +
116A GLN* 3.8 7.2 - - - +
131A ASP* 4.8 1.1 - - - -
132A ARG* 2.8 37.7 + - - +
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Residues in contact with LYS 47 (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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46A ALA* 1.3 73.6 - - - +
48A TRP* 1.3 64.8 + - - +
110A TYR* 3.9 1.6 - - - -
111A ILE* 3.1 21.7 + - + +
116A GLN* 2.8 69.5 + - - +
117A PHE* 3.4 15.7 + - - +
119A PRO* 3.5 22.4 - - + -
129A ILE* 4.0 10.8 - - + -
130A GLU 3.3 7.4 - - - +
131A ASP* 3.5 28.0 - - - +
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Residues in contact with TRP 48 (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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23A PRO* 3.9 30.4 - - + +
43A TYR* 5.7 3.4 - + - -
46A ALA* 3.6 19.6 + - - +
47A LYS* 1.3 80.8 - - - +
49A VAL* 1.3 58.4 + - - +
50A SER* 4.1 11.7 - - - +
88A PRO* 3.7 13.9 - - + -
90A THR* 3.6 27.8 - - + -
108A SER* 3.6 17.3 - - - -
109A LEU 3.3 9.4 - - - -
110A TYR* 3.2 45.4 - + + -
111A ILE* 3.9 4.9 - - - +
129A ILE* 3.5 3.8 - - - +
130A GLU* 2.6 42.2 + - + +
132A ARG* 3.3 47.1 - - + +
193A TRP* 5.1 4.7 - + - -
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Residues in contact with VAL 49 (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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48A TRP* 1.3 73.8 - - - +
50A SER* 1.3 61.6 + - - +
69A LEU* 3.5 13.1 - - + +
72A TYR* 3.8 38.6 - - + -
73A ILE* 4.7 6.7 - - + -
108A SER* 3.2 2.9 - - - -
109A LEU* 2.9 56.6 + - + +
111A ILE* 3.9 13.5 - - + +
127A VAL* 3.6 27.1 - - + -
128A PHE 3.6 5.8 - - - +
129A ILE* 4.3 7.4 - - + +
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Residues in contact with SER 50 (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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48A TRP* 4.1 1.0 - - - +
49A VAL* 1.3 76.3 - - - +
51A THR* 1.3 64.5 + - - +
69A LEU* 3.8 3.8 - - - -
106A THR* 3.9 4.9 - - - -
107A ILE 3.2 8.7 - - - -
108A SER* 2.8 22.0 + - - -
127A VAL* 3.4 3.3 - - - +
128A PHE* 2.7 62.7 + - - -
130A GLU* 2.9 21.8 + - - +
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Residues in contact with THR 51 (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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50A SER* 1.3 77.3 - - - +
52A SER* 1.3 66.5 + - - +
53A VAL* 5.7 2.2 - - + +
65A GLY* 3.7 37.5 - - - +
68A LYS* 4.0 19.7 + - + +
69A LEU* 4.0 13.0 - - + -
105A ILE 3.9 0.7 - - - +
106A THR* 3.3 1.2 - - - -
107A ILE* 2.7 41.7 + - + +
126A ASP* 2.7 26.5 + - - +
127A VAL* 4.2 6.1 - - - -
128A PHE* 4.2 1.8 - - - -
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Residues in contact with SER 52 (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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51A THR* 1.3 78.4 + - - +
53A VAL* 1.3 69.7 + - - +
68A LYS* 5.2 2.4 + - - -
104A THR* 4.3 11.7 - - - +
105A ILE 3.3 5.6 - - - -
106A THR* 2.8 27.6 + - - +
126A ASP* 4.2 7.5 + - - +
128A PHE* 3.9 15.0 - - - -
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Residues in contact with VAL 53 (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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51A THR* 5.7 2.2 - - + +
52A SER* 1.3 81.6 - - - +
54A GLU* 1.3 65.8 + - - +
55A SER* 3.6 15.2 + - - -
61A ALA* 3.6 32.3 - - + +
64A THR* 4.5 23.1 - - + -
65A GLY* 5.3 4.7 - - - +
68A LYS* 4.8 10.5 - - - +
103A SER 3.6 0.5 - - - +
104A THR* 3.4 3.1 - - - -
105A ILE* 2.7 43.7 + - + +
107A ILE* 4.9 4.3 - - + -
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Residues in contact with GLU 54 (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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53A VAL* 1.3 72.6 - - - +
55A SER* 1.3 65.9 + - - +
96A GLY 5.5 2.8 - - - +
102A GLU* 4.0 29.8 + - + +
103A SER 3.3 8.5 - - - +
104A THR* 2.6 36.2 + - - +
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Residues in contact with SER 55 (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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53A VAL* 3.6 18.5 + - - -
54A GLU* 1.3 76.6 - - - +
56A MET* 1.3 65.9 + - - +
57A ASP* 2.9 24.5 + - - +
60A SER* 5.2 1.4 - - - -
61A ALA* 4.1 11.2 + - - +
102A GLU* 3.7 12.1 - - - +
103A SER* 2.9 33.2 + - - +
105A ILE* 4.4 8.1 - - - +
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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