Contacts of the strand formed by residues 139 - 145 (chain B) in PDB entry 6CO1
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 VAL 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B GLN* 3.6 46.0 - - + +
54B MET 3.9 2.7 - - - +
55B ARG* 5.0 0.2 - - - +
85B GLY* 5.1 5.2 - - - +
134B ASP* 3.3 34.9 + - - +
135B HIS* 3.6 7.3 + - - +
136B GLY 2.8 31.4 + - - -
138B GLU* 1.3 82.2 - - + +
140B LEU* 1.3 60.8 + - - +
141B GLY 3.8 11.4 + - - +
142B LEU* 3.9 17.7 - - + -
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Residues in contact with LEU 140 (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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126A GLU* 5.0 0.5 - - - +
142A LEU 3.9 0.5 - - - +
143A VAL* 3.4 3.8 - - - -
144A ARG* 3.0 62.3 + - + +
145A VAL 5.0 0.2 - - - -
146A PRO* 3.9 29.2 - - + -
148A TYR* 4.6 4.7 - - + +
54B MET* 2.9 21.1 + - + +
55B ARG 3.3 26.7 - - - +
56B PHE* 4.0 4.9 - - - -
135B HIS* 4.6 7.8 - - - -
136B GLY* 4.3 15.7 - - - +
137B LEU 3.9 17.7 - - - +
139B VAL* 1.3 78.8 - - - +
141B GLY* 1.3 55.6 + - - +
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Residues in contact with GLY 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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142A LEU 3.3 15.3 - - - -
143A VAL* 4.5 3.0 - - - +
53B GLN* 3.2 3.6 - - - +
54B MET* 2.8 28.4 + - - +
135B HIS* 4.8 10.7 + - - -
139B VAL* 3.4 7.1 + - - +
140B LEU* 1.3 79.8 - - - +
142B LEU* 1.3 68.4 + - - -
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Residues in contact with LEU 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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141A GLY* 3.4 17.3 - - - -
142A LEU 3.9 3.5 + - - +
51B LEU* 4.4 28.5 - - + -
52B MET 3.3 12.6 - - - +
53B GLN* 4.2 9.4 - - + +
63B PRO* 5.7 2.7 - - + -
85B GLY 5.1 0.9 - - - +
86B LEU* 3.9 19.5 - - + -
125B VAL 4.6 0.7 - - - +
126B GLU* 4.4 17.9 - - + -
129B ALA* 3.7 34.8 - - + -
135B HIS* 6.3 0.4 - - - +
139B VAL* 3.9 20.0 - - + -
141B GLY* 1.3 80.1 - - - +
143B VAL* 1.3 67.4 + - - +
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Residues in contact with VAL 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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54A MET* 3.8 28.7 - - + -
140A LEU 3.2 8.5 - - - +
141A GLY* 4.5 2.5 - - - -
143A VAL* 3.8 26.5 - - + -
50B VAL 3.6 1.2 - - - +
51B LEU* 3.6 5.1 - - - +
52B MET* 2.8 52.4 + - + +
53B GLN 4.4 1.8 - - - +
54B MET 5.2 1.3 - - - +
60B LEU* 4.6 12.8 - - + -
126B GLU* 5.2 0.4 - - - -
141B GLY 4.6 2.0 - - - +
142B LEU* 1.3 80.6 - - - +
144B ARG* 1.3 62.1 + - - +
160B PHE* 4.3 20.4 - - + -
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Residues in contact with ARG 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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54A MET* 4.6 0.9 - - - +
135A HIS* 4.1 7.9 + - - +
136A GLY* 3.5 35.8 + - - -
140A LEU* 2.9 39.0 + - + +
36B ASN* 4.2 4.8 - - - +
49B SER* 4.0 26.8 + - - +
50B VAL 3.2 6.5 - - - +
51B LEU* 4.2 7.2 - - + -
119B LEU* 4.0 24.8 + - - +
122B LEU* 4.5 5.1 - - + +
123B HIS* 4.0 21.4 - - - +
126B GLU* 2.9 43.4 + - - +
143B VAL* 1.3 77.7 - - - +
145B VAL* 1.3 66.8 + - - +
146B PRO* 3.4 8.8 - - - +
160B PHE* 4.6 1.9 - - - -
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Residues in contact with VAL 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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140A LEU* 4.9 0.2 - - - -
48B PHE 4.3 8.1 - - - +
49B SER* 4.7 1.2 - - - -
50B VAL* 2.9 39.5 + - + +
52B MET* 3.7 26.5 - - + -
144B ARG* 1.3 73.0 - - - +
146B PRO* 1.3 65.1 - - + +
147B LEU* 3.4 18.2 + - + +
157B PHE* 3.9 21.8 - - + -
160B PHE* 3.6 39.9 - - + -
173B LEU* 4.4 7.0 - - + -
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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