Contacts of the strand formed by residues 71 - 78 (chain L) in PDB entry 1VCB
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 PRO 71 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69L ARG 3.2 11.7 - - - +
70L GLU* 1.3 86.3 - - + +
72L SER* 1.3 59.4 + - - +
110L HIS* 6.5 0.7 - - + -
111L SER 3.6 8.7 - - - +
112L TYR* 3.7 13.0 - - + -
113L ARG* 4.7 5.0 - - - +
141L ASN* 4.3 8.2 + - - +
142L VAL* 5.7 3.3 - - - +
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Residues in contact with SER 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70L GLU 3.5 0.2 + - - -
71L PRO* 1.3 75.6 - - - +
73L GLN* 1.3 63.5 + - - +
74L VAL* 3.6 1.6 + - - +
110L HIS* 5.1 0.7 - - - -
111L SER* 2.9 34.3 + - - -
112L TYR 3.7 22.4 - - - -
113L ARG* 3.7 2.9 - - - -
138L PRO* 3.6 16.1 - - - +
139L SER 2.7 27.9 + - - -
141L ASN* 3.8 10.0 + - - -
147L ILE* 4.2 4.2 - - - +
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Residues in contact with GLN 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71L PRO 4.3 0.2 - - - -
72L SER* 1.3 71.6 - - - +
74L VAL* 1.3 63.4 + - - +
108L ARG* 2.9 45.7 + - + +
109L ILE 3.7 10.1 - - - +
110L HIS* 3.5 22.6 + - + +
141L ASN* 2.5 40.4 + - - +
145L GLN* 4.3 12.9 + - - +
146L PRO* 3.5 16.3 - - + +
147L ILE* 3.1 14.6 + - - +
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Residues in contact with VAL 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72L SER* 4.0 8.3 - - - +
73L GLN* 1.3 80.1 - - - +
75L ILE* 1.3 72.2 + - - +
76L PHE* 3.8 20.2 - - + -
108L ARG* 3.5 7.1 - - - +
109L ILE* 2.6 48.6 + - + +
111L SER* 4.2 4.7 - - - -
117L TRP* 5.9 0.2 - - - +
136L PHE* 3.4 27.6 - - + -
138L PRO* 3.7 36.6 - - + -
146L PRO* 5.3 1.3 - - - -
147L ILE* 3.4 15.0 - - + +
149L ALA* 4.2 1.1 - - + -
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Residues in contact with ILE 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74L VAL* 1.3 79.6 - - - +
76L PHE* 1.3 65.2 + - - +
77L CYS* 3.3 6.6 + - + -
106L GLY* 5.4 1.8 - - - -
107L ARG 3.5 16.6 - - - +
108L ARG* 4.8 8.7 - - + +
146L PRO* 4.4 13.7 - - + -
147L ILE 2.9 17.2 + - - +
148L PHE* 3.2 51.8 - - + -
149L ALA* 2.9 29.5 + - - +
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Residues in contact with PHE 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74L VAL* 3.8 20.2 - - + -
75L ILE* 1.3 73.6 - - - +
77L CYS* 1.4 59.2 + - - +
78L ASN 3.5 1.8 + - - -
86L PRO* 3.7 26.9 - - + -
98L TYR* 5.7 1.3 - + + -
101L LEU* 3.7 22.5 - - + +
106L GLY* 3.1 20.5 - - - -
107L ARG* 2.8 21.5 + - + +
109L ILE* 3.5 31.9 - - + -
117L TRP* 3.8 38.6 - + - -
119L PHE* 3.6 24.9 - + - -
136L PHE* 4.5 5.6 - + - -
149L ALA* 3.8 18.2 - - + -
151L ILE* 4.3 3.1 - - + -
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Residues in contact with CYS 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L ILE* 3.3 5.6 + - + -
76L PHE* 1.4 70.7 - - - +
78L ASN* 1.3 60.4 + - - +
79L ARG* 3.3 29.9 + - - +
104L GLY 5.3 3.4 - - - -
105L THR 4.6 2.7 - - - -
106L GLY* 4.0 13.7 - - - -
148L PHE* 3.5 33.2 - - + -
149L ALA 3.1 9.1 + - - +
150L ASN* 3.7 3.0 - - - +
151L ILE* 3.0 27.3 + - - +
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Residues in contact with ASN 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L PHE 3.5 2.0 + - - -
77L CYS* 1.3 69.5 - - - +
79L ARG* 1.3 58.5 + - - +
80L SER* 2.9 29.1 + - - -
82L ARG 3.0 20.2 + - - -
84L VAL* 3.3 15.2 - - + +
101L LEU* 3.5 22.3 + - + -
102L PRO 2.8 27.0 + - - +
103L PRO 3.4 15.9 - - - +
104L GLY* 3.6 14.0 - - - +
105L THR 2.9 20.0 + - - +
151L ILE* 4.1 6.9 - - + +
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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