Contacts of the strand formed by residues 71 - 78 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I ARG 3.2 11.7 - - - +
70I GLU* 1.3 86.2 - - - +
72I SER* 1.3 59.1 + - - +
110I HIS* 6.5 0.9 - - + -
111I SER 3.6 9.0 - - - +
112I TYR* 3.6 12.8 - - + -
113I ARG* 4.7 5.0 - - - +
141I ASN* 4.3 8.2 + - - +
142I VAL* 5.6 3.8 - - - +
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Residues in contact with SER 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I GLU 3.5 0.2 + - - -
71I PRO* 1.3 74.6 - - - +
73I GLN* 1.3 63.4 + - - +
74I VAL* 3.6 2.0 + - - +
110I HIS* 5.1 0.7 - - - -
111I SER* 2.9 33.8 + - - -
112I TYR 3.7 22.2 - - - -
113I ARG* 3.7 3.6 - - - -
138I PRO* 3.5 17.3 - - - +
139I SER 2.8 26.5 + - - -
141I ASN* 3.8 9.9 + - - +
147I ILE* 4.2 4.7 - - - +
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Residues in contact with GLN 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I PRO 4.3 0.4 - - - -
72I SER* 1.3 71.5 - - - +
74I VAL* 1.3 63.8 + - - +
108I ARG* 3.0 44.9 + - + +
109I ILE 3.7 10.3 - - - +
110I HIS* 3.5 23.5 + - + +
141I ASN* 2.5 39.9 + - - +
145I GLN* 4.4 12.7 + - - +
146I PRO* 3.5 16.3 - - + +
147I ILE* 3.0 15.2 + - - +
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Residues in contact with VAL 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I SER* 3.9 9.0 - - - +
73I GLN* 1.3 78.8 - - - +
75I ILE* 1.3 71.4 + - - +
76I PHE* 3.8 20.6 - - + -
108I ARG* 3.5 6.4 - - - +
109I ILE* 2.6 49.2 + - + +
111I SER* 4.2 5.4 - - - -
136I PHE* 3.4 26.9 - - + -
138I PRO* 3.7 36.8 - - + -
146I PRO* 5.3 1.3 - - - -
147I ILE* 3.4 15.0 - - + +
149I ALA* 4.1 1.1 - - + -
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Residues in contact with ILE 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I VAL* 1.3 76.1 - - - +
76I PHE* 1.3 67.0 + - - +
77I CYS* 3.3 7.3 + - + +
106I GLY* 5.4 2.0 - - - -
107I ARG 3.5 15.3 - - - +
108I ARG* 4.8 8.5 - - + +
146I PRO* 4.4 13.7 - - + -
147I ILE 2.9 20.4 + - - +
148I PHE* 3.2 51.7 - - + -
149I ALA 2.8 28.9 + - - -
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Residues in contact with PHE 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I VAL* 3.8 20.0 - - + -
75I ILE* 1.3 72.7 - - - +
77I CYS* 1.4 60.0 + - - +
78I ASN 3.5 1.8 + - - -
86I PRO* 3.7 27.1 - - + -
98I TYR* 5.6 1.3 - + + -
101I LEU* 3.7 22.3 - - + +
106I GLY* 3.1 20.1 - - - -
107I ARG* 2.8 21.7 + - + +
109I ILE* 3.5 30.5 - - + -
117I TRP* 3.7 39.0 - + - -
119I PHE* 3.6 24.9 - + - -
136I PHE* 4.5 5.8 - + - -
149I ALA* 3.8 18.4 - - + -
151I ILE* 4.3 2.7 - - + -
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Residues in contact with CYS 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I ILE* 3.3 5.7 + - + -
76I PHE* 1.4 71.5 - - - +
78I ASN* 1.3 61.7 + - - +
79I ARG* 3.3 30.0 + - - +
104I GLY 5.3 3.6 - - - -
105I THR 4.6 2.9 - - - -
106I GLY* 4.1 12.6 - - - -
148I PHE* 3.5 34.8 - - + -
149I ALA 3.1 9.1 + - - +
150I ASN* 3.8 3.5 - - - +
151I ILE* 3.0 27.9 + - - +
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Residues in contact with ASN 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I PHE 3.5 2.0 + - - -
77I CYS* 1.3 69.7 - - - +
79I ARG* 1.3 58.3 + - - +
80I SER* 2.9 28.9 + - - -
82I ARG 3.0 20.2 + - - -
84I VAL* 3.3 14.8 - - + +
101I LEU* 3.5 22.1 + - + -
102I PRO 2.7 27.4 + - - +
103I PRO 3.4 16.3 - - - +
104I GLY* 3.6 14.2 - - - +
105I THR 2.9 19.3 + - - +
151I ILE* 4.1 6.8 - - + +
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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