Contacts of the strand formed by residues 71 - 78 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ARG 3.2 11.4 - - - +
70F GLU* 1.3 86.4 - - + +
72F SER* 1.3 60.5 + - - +
73F GLN 4.3 0.4 - - - -
110F HIS* 6.5 0.7 - - + -
111F SER 3.6 8.7 - - - +
112F TYR* 3.7 13.7 - - + -
113F ARG* 4.6 5.2 - - - +
141F ASN* 4.3 8.0 + - - +
142F VAL* 5.6 3.8 - - - +
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Residues in contact with SER 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F GLU 3.5 0.2 + - - -
71F PRO* 1.3 75.5 - - - +
73F GLN* 1.3 62.2 + - - +
74F VAL* 3.6 2.4 + - - +
110F HIS* 5.1 0.2 - - - -
111F SER* 2.9 33.1 + - - -
112F TYR 3.7 5.2 - - - -
113F ARG* 3.7 20.9 - - - -
138F PRO* 3.6 16.8 - - - +
139F SER 2.8 26.8 + - - -
141F ASN* 3.8 10.3 + - - -
147F ILE* 4.2 4.2 - - - +
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Residues in contact with GLN 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F PRO 4.3 0.4 - - - -
72F SER* 1.3 72.3 - - - +
74F VAL* 1.3 63.5 + - - +
108F ARG* 3.0 44.2 + - + +
109F ILE 3.7 11.0 - - - +
110F HIS* 3.5 23.2 + - + +
141F ASN* 2.5 40.8 + - - +
145F GLN* 4.4 12.6 + - - +
146F PRO* 3.4 17.2 - - + +
147F ILE* 3.0 14.6 + - - +
111H ASP* 4.6 10.4 + - - +
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Residues in contact with VAL 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F SER* 3.9 9.4 - - - +
73F GLN* 1.3 79.0 - - - +
75F ILE* 1.3 72.3 + - - +
76F PHE* 3.8 21.5 - - + -
108F ARG* 3.5 6.3 - - - +
109F ILE* 2.6 47.7 + - + +
111F SER* 4.2 6.3 - - - -
136F PHE* 3.4 26.7 - - + -
138F PRO* 3.7 36.1 - - + -
146F PRO* 5.3 1.6 - - - -
147F ILE* 3.4 14.6 - - + +
149F ALA* 4.1 0.9 - - + -
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Residues in contact with ILE 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F VAL* 1.3 79.2 - - - +
76F PHE* 1.3 68.3 + - - +
77F CYS* 3.3 5.1 + - + +
106F GLY* 5.4 0.4 - - - -
107F ARG 3.5 16.2 - - - +
108F ARG* 4.8 7.2 - - + +
146F PRO* 4.4 12.6 - - + -
147F ILE 2.9 16.6 - - - +
148F PHE* 3.2 50.8 - - + -
149F ALA* 2.9 29.5 + - - +
41H THR* 3.8 33.0 - - + +
44H ALA* 5.0 0.4 - - + -
45H MET* 4.5 2.7 - - + -
109H PHE* 5.0 5.4 - - + -
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Residues in contact with PHE 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F VAL* 3.8 19.7 - - + -
75F ILE* 1.3 73.0 - - - +
77F CYS* 1.3 60.8 + - - +
78F ASN 3.6 0.9 + - - -
86F PRO* 3.7 27.4 - - + -
98F TYR* 5.7 0.9 - + + -
101F LEU* 3.7 23.4 - - + +
106F GLY* 3.0 20.6 - - - -
107F ARG* 2.8 21.2 + - + +
109F ILE* 3.5 29.6 - - + -
117F TRP* 3.8 38.4 - + - -
119F PHE* 3.6 23.8 - + - -
136F PHE* 4.5 6.3 - + - -
149F ALA* 3.7 17.5 - - + -
151F ILE* 4.2 2.9 - - + -
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Residues in contact with CYS 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F ILE* 3.3 4.6 + - + -
76F PHE* 1.3 72.1 - - - +
78F ASN* 1.3 61.3 + - - +
79F ARG* 3.3 26.8 + - - +
104F GLY 5.4 3.1 - - - -
105F THR 4.6 2.5 - - - -
106F GLY* 4.0 13.2 - - - -
148F PHE* 3.5 26.7 - - + -
149F ALA 3.0 10.1 + - - +
150F ASN* 3.7 2.3 - - - +
151F ILE* 3.0 27.6 + - - +
45H MET* 3.8 28.7 - - - -
63H ARG* 6.1 2.9 - - - -
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Residues in contact with ASN 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F PHE 3.6 1.8 + - - -
77F CYS* 1.3 70.0 - - - +
79F ARG* 1.3 57.9 + - - +
80F SER* 2.9 27.9 + - - -
82F ARG 3.0 19.8 + - - -
84F VAL* 3.3 15.7 - - + +
101F LEU* 3.5 24.1 + - + -
102F PRO 2.7 27.4 + - - +
103F PRO 3.4 15.2 + - - +
104F GLY* 3.6 14.3 - - - +
105F THR 2.9 19.3 + - - +
151F ILE* 4.1 7.1 - - + +
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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