Contacts of the strand formed by residues 152 - 158 (chain C) 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 LEU 152 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ALA* 4.0 10.8 - - - +
51C LYS* 4.3 4.3 - - + -
52C GLY* 3.9 23.3 - - - +
55C VAL* 3.8 31.2 - - + -
64C SER* 3.1 20.9 - - - +
66C SER* 3.9 18.2 - - - +
115C THR* 4.1 9.6 - - - +
117C VAL* 4.8 2.9 - - + -
146C VAL* 3.8 19.3 - - + +
147C MET* 4.1 17.0 - - - +
149C GLU* 2.9 32.5 + - + +
151C PRO* 1.3 81.4 - - + +
153C ARG* 1.3 61.8 + - - +
154C PRO* 4.7 0.4 - - - +
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Residues in contact with ARG 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C LYS 5.2 3.4 + - - -
63C ALA* 3.6 29.8 - - + +
64C SER 2.9 8.4 + - - +
65C THR* 3.5 4.0 - - - -
66C SER 3.1 22.2 + - - -
146C VAL* 4.8 2.5 - - - -
151C PRO 4.1 2.2 + - - +
152C LEU* 1.3 75.7 - - - +
154C PRO* 1.3 71.7 - - + +
305C ASP* 2.7 33.1 + - - -
306C VAL 2.8 31.4 + - - -
307C VAL* 3.4 28.9 - - - +
340C ILE* 3.6 20.2 - - + +
342C LYS* 4.3 12.3 - - - +
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Residues in contact with PRO 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C SER 3.6 7.6 - - - +
68C LEU* 5.3 3.4 - - + -
143C VAL* 4.1 20.2 - - + -
146C VAL* 4.5 18.4 - - + -
147C MET* 4.0 28.0 - - + -
152C LEU 4.7 0.7 - - - +
153C ARG* 1.3 83.9 - - - +
155C LEU* 1.3 59.2 + - - +
156C VAL* 3.9 12.0 + - + +
167C VAL* 5.4 2.1 - - + +
171C VAL* 4.6 9.4 - - + -
266C TYR* 5.6 0.2 - - - -
307C VAL 3.6 16.6 - - - +
308C GLY* 3.4 4.6 - - - -
309C ALA 3.2 21.5 + - - +
340C ILE* 4.7 3.0 - - - +
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Residues in contact with LEU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C THR* 3.7 30.3 - - + -
66C SER 3.1 6.8 + - - +
67C LEU* 3.2 10.6 - - + +
68C LEU 3.0 22.0 + - - -
153C ARG 3.6 1.0 + - - -
154C PRO* 1.3 71.0 - - - +
156C VAL* 1.3 73.8 + - - +
157C LEU* 3.7 19.0 + - + -
309C ALA* 3.1 19.1 - - + +
311C VAL* 4.3 9.9 - - + -
333C VAL* 3.5 39.0 - - + +
336C LEU* 3.8 16.4 - - + -
337C ALA 4.0 2.5 - - - +
340C ILE* 4.3 4.3 - - + -
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Residues in contact with VAL 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C LEU* 3.1 34.1 - - + +
70C VAL* 3.9 14.1 - - + -
143C VAL* 4.4 2.0 - - + -
154C PRO* 4.8 6.7 - - + -
155C LEU* 1.3 73.3 - - - +
157C LEU* 1.3 62.3 + - - +
163C ILE* 3.5 31.0 - - + -
167C VAL* 3.8 34.5 - - + -
309C ALA 2.8 12.4 + - - +
310C ASP* 3.1 31.4 - - + +
311C VAL 3.1 7.4 + - - -
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C LEU* 3.9 27.1 - - + -
68C LEU 3.0 6.8 + - - +
69C GLY* 3.4 2.9 - - - -
70C VAL 2.8 31.2 + - - -
86C PRO* 3.6 33.7 - - + +
89C ILE* 4.3 17.0 - - + -
90C ARG* 4.1 20.0 - - + +
155C LEU* 3.9 17.9 - - + +
156C VAL* 1.3 71.2 - - - +
158C GLY* 1.3 62.9 + - - +
311C VAL* 3.8 5.4 - - + -
333C VAL* 3.4 33.2 - - + -
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Residues in contact with GLY 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PRO 4.1 0.2 - - - -
85C ALA* 3.6 20.9 - - - +
86C PRO* 3.6 8.7 - - - +
89C ILE* 4.5 2.9 - - - +
156C VAL 3.7 2.6 + - - -
157C LEU* 1.3 78.8 - - - +
159C GLY* 1.3 70.9 + - - -
163C ILE* 3.4 17.9 - - - +
311C VAL 2.8 18.9 + - - +
312C VAL* 4.1 2.2 - - - -
313C GLU 5.1 0.4 - - - -
314C PHE* 5.6 0.7 - - - +
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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