Contacts of the strand formed by residues 138 - 148 (chain B) in PDB entry 6M6A
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 LEU 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ILE* 4.8 11.4 - - + -
59B GLU* 3.6 4.6 - - - +
71B VAL* 6.4 0.2 - - + -
78B ILE* 6.6 0.4 - - + -
101B LEU* 4.1 17.5 - - + +
102B LYS* 2.7 33.8 - - - +
103B ALA* 2.3 51.6 + - + +
109B VAL* 4.4 29.4 - - + -
132B LEU* 4.5 9.4 - - + -
137B ARG* 1.3 79.9 + - - +
139B ASN* 1.3 69.0 + - - +
140B MET* 4.5 15.5 - - + -
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Residues in contact with ASN 139 (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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57B TYR* 6.2 1.2 - - - -
58B ILE* 3.6 3.6 - - - +
59B GLU* 2.5 75.4 + - + +
100B LEU* 5.9 0.3 - - - +
101B LEU 3.5 3.9 - - - +
102B LYS* 4.5 11.7 - - + +
138B LEU* 1.3 71.9 - - - +
140B MET* 1.3 69.5 + - - +
141B GLU* 5.5 2.1 - - - +
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Residues in contact with MET 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 4.4 10.5 - - + -
57B TYR 3.2 7.9 - - - +
58B ILE* 4.4 10.3 - - + -
78B ILE* 5.8 4.7 - - + -
82B LEU* 4.8 11.2 - - + -
100B LEU* 3.3 26.6 - - - +
101B LEU* 2.9 33.9 + - - +
109B VAL* 5.8 2.9 - - - -
114B PHE* 3.5 29.4 - - + -
138B LEU* 4.5 16.8 - - + -
139B ASN* 1.3 84.8 + - - +
141B GLU* 1.3 66.0 + - - +
142B VAL* 3.8 27.6 - - + -
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Residues in contact with GLU 141 (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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56B VAL* 3.3 9.5 - - - +
57B TYR* 2.3 77.8 + - + +
98B THR* 4.4 11.0 - - + +
99B LEU 3.3 6.3 - - - -
100B LEU* 3.7 17.0 - - + -
139B ASN* 5.5 2.2 - - - +
140B MET* 1.3 75.5 - - - +
142B VAL* 1.3 60.4 + - - +
160B ASP* 5.3 5.2 - - - +
161B ARG* 2.8 52.4 + - - +
164B ALA* 5.3 2.9 - - + +
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Residues in contact with VAL 142 (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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53B VAL* 3.7 26.2 - - + -
55B SER 3.4 4.7 - - - -
56B VAL* 3.7 9.4 - - + -
82B LEU* 4.4 9.4 - - + -
85B LEU* 5.1 2.7 - - + -
97B VAL 3.7 1.0 - - - +
98B THR* 3.3 2.8 - - - +
99B LEU* 2.5 68.1 + - + +
114B PHE* 4.1 11.0 - - + -
140B MET* 3.8 21.1 - - + -
141B GLU* 1.3 77.7 - - - +
143B ARG* 1.3 60.4 + - - +
144B VAL* 4.0 13.0 - - + -
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Residues in contact with ARG 143 (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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53B VAL* 3.3 2.3 - - - +
54B THR* 2.4 45.7 + - - +
55B SER* 2.5 24.8 + - - +
96B THR* 2.3 44.0 + - - +
97B VAL 3.3 11.6 - - - -
98B THR* 2.4 38.4 + - + +
142B VAL* 1.3 71.8 - - - +
144B VAL* 1.3 53.5 + - - +
145B ASP* 3.1 11.5 + - - +
158B ILE* 3.8 13.2 - - + -
160B ASP* 2.8 33.1 + - - +
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Residues in contact with VAL 144 (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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51B THR* 4.5 5.4 - - - +
52B ALA 3.3 23.8 - - - +
53B VAL* 3.7 18.8 - - + +
85B LEU* 5.0 7.6 - - + -
87B VAL* 4.5 12.6 - - + -
89B PHE* 3.6 16.3 - - + -
96B THR* 3.3 1.6 - - - -
97B VAL* 2.7 42.2 + - + +
99B LEU* 3.7 22.2 - - + -
120B VAL* 6.3 0.4 - - + -
142B VAL* 4.0 8.5 - - + -
143B ARG* 1.3 75.6 - - - +
145B ASP* 1.3 64.1 + - - +
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Residues in contact with ASP 145 (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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51B THR* 3.2 7.4 - - - -
52B ALA 2.7 30.3 + - - -
54B THR* 3.1 33.6 + - + +
89B PHE* 3.8 2.2 - - - -
95B GLN 3.2 9.9 - - - +
96B THR* 2.4 30.8 + - - +
143B ARG* 3.1 9.4 + - - -
144B VAL* 1.3 75.9 - - - +
146B ARG* 1.3 62.7 + - - +
156B HIS* 6.1 0.7 - - - +
158B ILE* 3.6 13.5 - - - +
171B PHE* 3.4 10.5 - - + -
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Residues in contact with ARG 146 (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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49B PRO* 5.3 8.7 - - - +
50B GLY* 3.2 22.7 - - - +
51B THR* 3.7 7.9 - - + -
89B PHE* 3.3 26.7 - - + +
91B ASN 2.7 23.2 + - - -
92B PRO* 3.1 22.5 + - - +
94B LEU 2.4 26.5 + - - -
95B GLN* 2.6 51.6 + - - +
145B ASP* 1.3 75.2 - - - +
147B GLY* 1.3 58.1 + - - +
171B PHE* 3.4 11.6 - - - -
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Residues in contact with GLY 147 (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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49B PRO* 3.2 5.1 - - - +
50B GLY 2.5 40.0 + - - +
146B ARG* 1.3 77.7 - - - +
148B VAL* 1.3 59.5 + - - -
171B PHE* 3.3 16.5 - - - -
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Residues in contact with VAL 148 (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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46B SER 3.5 17.0 - - - +
47B SER* 3.9 9.9 - - - +
48B ILE 3.3 30.3 - - - +
49B PRO* 3.7 9.2 - - + -
147B GLY* 1.3 76.8 - - - +
149B GLY* 1.3 69.0 + - - +
150B TYR 4.8 2.1 - - - +
151B VAL* 5.5 1.2 - - - +
171B PHE* 3.2 12.9 - - - -
172B SER* 3.6 0.2 - - - -
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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