Contacts of the strand formed by residues 112 - 118 (chain P) in PDB entry 1VF5
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 ASN 112 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77P MET* 3.6 0.2 - - - -
78P LEU* 2.6 65.7 + - + +
79P PRO 3.6 12.1 - - - +
80P GLU* 4.1 23.8 + - - +
81P GLY 4.4 5.1 + - - +
82P PHE 2.8 22.4 + - - +
110P GLN* 4.1 9.1 - - - +
111P ASP* 1.3 85.2 + - - +
113P VAL* 1.3 75.6 + - - +
114P LEU* 4.0 1.6 - - - -
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Residues in contact with VAL 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P PRO* 4.2 13.0 - - + -
75P VAL* 4.9 5.2 - - + -
76P LEU 3.2 11.4 - - - +
77P MET* 3.8 27.4 - - + -
105P PRO* 3.4 5.4 - - - +
106P TYR* 2.9 34.6 + - + -
110P GLN* 3.2 34.8 + - + +
111P ASP 3.3 0.2 - - - -
112P ASN* 1.3 103.3 - - - +
114P LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75P VAL* 3.6 3.9 - - - +
76P LEU* 3.0 34.1 + - + +
78P LEU* 4.4 13.7 - - + -
84P ILE* 3.7 35.4 - - + +
103P PHE* 4.0 22.0 - - + +
104P GLN 3.7 3.4 - - - +
105P PRO* 4.5 10.8 - - + -
106P TYR* 5.9 0.4 - - - -
110P GLN 4.4 0.7 - - - +
111P ASP* 2.9 35.0 - - - +
112P ASN 4.5 1.8 - - - +
113P VAL* 1.3 82.0 - - - +
115P LEU* 1.3 61.6 + - - +
116P VAL* 4.0 1.1 + - - +
129P PHE* 4.1 22.5 - - + -
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Residues in contact with LEU 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2P PRO* 3.5 31.4 - - + +
3P PHE* 4.5 1.3 - - - +
6P GLN* 3.4 36.3 - - + +
74P ALA 3.9 6.1 - - - +
75P VAL* 4.0 13.0 - - + -
102P TYR 3.7 1.7 - - - +
103P PHE* 3.7 1.9 - - - -
104P GLN* 2.8 47.0 + - + +
106P TYR* 3.8 23.3 - - + -
114P LEU* 1.3 73.8 - - - +
116P VAL* 1.3 59.8 + - - +
117P GLY 3.0 6.2 + - - -
301P HEM 3.8 28.9 - - + -
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Residues in contact with VAL 116 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2P PRO* 3.6 10.7 - - - +
73P GLY* 4.2 6.1 - - - -
74P ALA* 3.4 27.4 + - + +
101P VAL* 4.2 9.9 - - + -
102P TYR 4.1 1.3 - - - -
103P PHE* 3.8 19.7 - - + -
114P LEU 4.0 1.5 + - - +
115P LEU* 1.3 71.4 - - - +
117P GLY* 1.3 59.0 + - - +
118P PRO* 2.6 44.6 - - + +
120P PRO* 4.8 2.9 - - + -
127P ILE* 4.7 19.7 - - + -
129P PHE* 3.4 35.2 - - + -
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Residues in contact with GLY 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2P PRO* 3.9 7.1 - - - +
3P PHE* 3.1 22.4 - - - -
104P GLN* 3.0 22.6 + - - -
115P LEU 3.0 8.3 + - - -
116P VAL* 1.3 75.4 - - - +
118P PRO* 1.3 73.0 - - - +
119P LEU* 2.8 20.4 - - - +
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Residues in contact with PRO 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P PHE* 4.3 0.2 - - - -
72P VAL 3.9 1.0 - - - +
101P VAL* 3.5 27.8 - - + -
102P TYR* 2.9 48.9 - - + +
104P GLN* 3.6 7.2 - - - +
116P VAL* 2.6 28.5 - - - +
117P GLY* 1.3 78.8 - - - +
119P LEU* 1.3 61.3 + - + +
120P PRO* 2.9 13.2 - - + +
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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