Contacts of the strand formed by residues 126 - 133 (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 GLU 126 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49P VAL* 3.4 27.2 - - + +
50P VAL 2.7 21.7 - - - +
51P LYS* 3.2 28.5 + - - +
98P VAL* 5.2 5.8 - - + -
123P GLN 5.1 3.6 - - - +
124P TYR* 2.8 3.4 - - - -
125P GLN 1.3 83.3 - - - +
127P ILE* 1.3 71.8 + - - +
128P VAL* 4.3 12.8 - - + -
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Residues in contact with ILE 127 (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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49P VAL* 3.7 0.7 - - - -
50P VAL* 3.0 23.2 + - + +
52P ILE* 3.6 22.9 - - + -
72P VAL* 3.6 20.0 - - + -
73P GLY 5.0 1.3 - - - +
74P ALA* 5.3 1.6 - - + -
99P GLY* 5.4 1.1 - - - -
101P VAL* 5.3 2.7 - - + -
103P PHE* 5.1 4.3 - - + -
116P VAL* 4.7 22.0 - - + -
120P PRO* 5.5 0.9 - - + -
124P TYR* 3.1 51.8 + - + +
126P GLU* 1.3 85.6 - - - +
128P VAL* 1.3 62.7 + - - +
129P PHE* 3.3 28.6 - - + -
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Residues in contact with VAL 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P LYS* 3.6 34.8 - - + +
48P ALA 3.9 2.5 - - - -
49P VAL* 3.7 19.3 - - + -
95P LYS* 5.1 7.4 - - + +
98P VAL* 3.4 39.5 - - + +
99P GLY* 4.3 21.3 - - - +
103P PHE* 3.6 15.8 - - - -
126P GLU* 4.3 11.2 - - + -
127P ILE* 1.3 74.4 - - - +
129P PHE* 1.3 72.1 + - - +
130P PRO* 4.0 4.5 - - + +
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Residues in contact with PHE 129 (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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46P PHE 3.5 4.2 - - - +
47P LYS* 3.6 2.4 - - - -
48P ALA* 3.0 48.8 + - + +
50P VAL* 3.6 20.2 - - + -
74P ALA* 5.4 3.1 - - + -
76P LEU* 3.5 37.2 - - + -
78P LEU* 5.8 1.8 - - + -
84P ILE* 4.1 5.4 - - + -
103P PHE* 4.2 13.9 - + - -
114P LEU* 4.1 25.4 - - + -
116P VAL* 3.4 31.0 - - + -
127P ILE* 3.3 24.5 - - + -
128P VAL* 1.3 81.9 - - - +
130P PRO* 1.3 66.3 - - + +
131P VAL* 3.5 6.3 + - + -
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Residues in contact with PRO 130 (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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45P VAL* 4.6 4.7 - - + -
46P PHE 3.4 8.1 - - - +
47P LYS* 5.1 0.4 - - - -
84P ILE* 3.4 26.9 - - + +
85P ALA* 2.9 21.5 + - - +
90P ILE* 3.8 23.8 - - + -
95P LYS* 4.0 30.3 - - + +
99P GLY 5.8 1.8 - - - +
103P PHE* 3.6 13.0 - - + -
128P VAL* 4.0 5.8 - - + +
129P PHE* 1.3 79.8 - - - +
131P VAL* 1.3 61.6 + - - +
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Residues in contact with VAL 131 (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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44P THR 3.6 0.9 - - - +
45P VAL* 3.3 4.0 - - - -
46P PHE* 2.8 67.9 + - + +
48P ALA* 3.8 21.8 - - + -
78P LEU* 3.8 29.2 - - + -
82P PHE* 3.8 18.8 - - + -
83P LYS 3.6 11.7 - - - +
84P ILE* 4.0 6.1 - - + +
85P ALA* 4.2 0.4 - - - -
129P PHE* 4.1 5.8 - - + +
130P PRO* 1.3 74.8 - - - +
132P LEU* 1.3 64.1 + - - +
133P SER 4.2 0.2 - - - -
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Residues in contact with LEU 132 (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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43P ASP* 3.7 10.5 - - - +
44P THR 3.5 24.0 - - - +
45P VAL* 4.1 2.2 - - + +
81P GLY 4.2 1.6 - - - +
82P PHE* 3.5 5.2 - - - -
83P LYS* 2.8 53.3 + - + +
84P ILE 4.4 0.2 - - - -
85P ALA* 3.8 13.2 - - + +
86P PRO* 3.9 23.1 - - + -
89P ARG* 3.1 35.0 - - - +
131P VAL* 1.3 76.3 - - - +
133P SER* 1.3 69.0 + - - +
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Residues in contact with SER 133 (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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40P VAL* 3.8 11.7 - - - -
41P LEU 2.8 20.6 + - - -
42P PRO* 4.5 1.1 - - - -
43P ASP* 3.0 21.5 + - - +
44P THR* 2.8 34.4 + - - -
46P PHE* 3.9 4.2 - - - -
82P PHE* 3.7 19.3 - - - -
132P LEU* 1.3 80.2 - - - +
134P PRO* 1.3 74.6 - - - +
249P LEU* 4.5 2.5 - - - -
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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