Contacts of the strand formed by residues 64 - 70 (chain A) in PDB entry 6VSU
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 SER 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A VAL* 3.5 18.8 - - - +
61A ALA* 3.7 5.9 - - - +
63A ALA* 1.3 73.7 + - - +
65A THR* 1.3 59.0 - - - +
111A PRO 4.0 8.7 - - - -
112A ARG* 2.5 36.5 + - - -
151A PRO* 3.0 13.0 + - - +
152A LEU* 3.2 15.4 - - - +
153A ARG* 2.8 30.7 + - - -
340A ILE* 5.1 0.2 - - - -
341A SER* 3.7 0.7 - - - -
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Residues in contact with THR 65 (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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64A SER* 1.3 70.8 - - - +
66A SER* 1.3 53.8 + - - +
67A LEU* 4.2 0.9 - - + -
113A VAL 3.5 7.7 + - - -
114A LEU* 3.3 11.1 - - + -
115A THR* 2.9 31.6 + - - +
153A ARG 3.5 7.2 - - - +
155A LEU* 3.6 33.2 - - + -
337A ALA* 3.0 34.3 + - + -
340A ILE* 3.4 19.2 - - + +
341A SER* 2.7 25.0 + - - +
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Residues in contact with SER 66 (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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64A SER 3.4 0.6 + - - -
65A THR* 1.3 69.5 - - - +
67A LEU* 1.3 64.0 - - - +
68A LEU* 3.7 1.2 + - - +
115A THR* 2.9 28.8 + - - -
117A VAL* 3.3 23.4 - - - +
146A VAL* 3.7 26.3 - - - +
152A LEU* 4.0 12.9 - - - +
153A ARG 2.9 9.7 + - - -
154A PRO* 3.5 6.6 - - - +
155A LEU 3.1 21.4 + - - -
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Residues in contact with LEU 67 (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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65A THR* 4.5 0.2 - - + -
66A SER* 1.3 70.5 - - - +
68A LEU* 1.3 58.9 + - - +
90A ARG* 5.0 2.2 - - + +
93A ILE* 3.9 26.0 - - + -
94A TRP* 5.9 2.7 - - - +
114A LEU* 3.6 28.5 - - + -
115A THR 3.2 5.5 + - - +
116A ASP* 3.4 32.2 - - + +
117A VAL* 2.9 32.4 + - - +
155A LEU* 3.1 26.9 - - + +
157A LEU* 4.3 17.0 - - + -
333A VAL* 3.6 24.2 - - + -
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Residues in contact with LEU 68 (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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44A ILE* 4.3 14.6 - - + -
66A SER 4.7 2.0 - - - +
67A LEU* 1.3 73.2 - - - +
69A GLY* 1.3 63.7 + - - +
70A VAL* 4.8 3.4 - - + -
90A ARG* 4.5 0.2 - - - -
117A VAL* 3.8 17.9 - - + -
118A GLY 3.6 13.2 - - - +
120A VAL* 3.9 21.1 - - + -
139A ILE 4.8 0.7 - - - +
142A SER* 3.9 11.4 - - - +
143A VAL* 3.8 43.3 - - + +
146A VAL* 4.4 8.7 - - + -
154A PRO* 5.6 3.1 - - + -
155A LEU 3.0 9.2 + - - +
156A VAL* 3.1 19.3 - - + +
157A LEU* 3.0 21.5 + - - -
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Residues in contact with GLY 69 (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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68A LEU* 1.3 71.4 - - - +
70A VAL* 1.3 57.1 - - - -
71A PRO* 3.6 4.5 - - - -
86A PRO* 4.1 5.6 - - - -
90A ARG* 3.5 7.9 - - - +
118A GLY 2.9 11.1 + - - -
119A ASP* 3.0 19.1 - - - -
120A VAL* 2.9 35.2 + - - +
157A LEU* 3.4 11.0 - - - -
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Residues in contact with VAL 70 (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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68A LEU* 4.3 7.9 - - + +
69A GLY* 1.3 75.5 - - - +
71A PRO* 1.3 58.2 - - - +
72A LEU* 2.8 14.0 + - + +
86A PRO* 4.3 0.4 - - - -
120A VAL* 4.5 8.1 - - + -
122A VAL* 4.1 10.8 - - + -
139A ILE* 3.4 50.0 - - + -
156A VAL* 3.7 22.7 - - + -
157A LEU 2.9 9.1 + - - -
158A GLY* 3.8 1.2 - - - -
159A GLY* 3.4 18.7 + - - -
163A ILE* 3.4 24.2 - - + -
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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