Contacts of the strand formed by residues 31 - 38 (chain D) in PDB entry 1VLP
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 THR 31 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D ASP 4.1 8.5 - - - +
30D VAL* 1.3 77.4 - - - +
32D VAL* 1.3 65.9 + - - +
123D GLY* 3.2 19.7 - - - +
124D SER* 4.2 5.2 - - - +
384D ASN* 2.8 35.4 + - - -
385D GLY 4.7 1.2 + - - -
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Residues in contact with VAL 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D VAL* 4.2 2.0 - - + -
31D THR* 1.3 81.3 - - - +
33D THR* 1.3 65.1 + - - +
34D TYR* 3.9 8.7 - - + -
122D SER* 3.3 2.9 - - - -
123D GLY 2.8 34.8 + - - +
125D TRP* 3.7 36.3 - - + -
128D THR* 3.0 30.1 - - - +
380D LEU* 3.9 6.3 - - + -
382D GLU* 3.3 11.4 - - - +
383D VAL* 3.8 26.2 - - + -
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Residues in contact with THR 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D VAL* 1.3 74.5 + - - +
34D TYR* 1.3 71.6 + - - +
120D LEU* 3.8 24.0 - - + -
121D VAL 3.2 3.8 - - - -
122D SER* 3.2 23.9 + - - +
380D LEU* 3.8 2.6 - - - +
381D LEU* 2.8 38.3 + - + +
382D GLU* 2.9 41.8 + - - +
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Residues in contact with TYR 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LYS* 4.9 4.0 - - - -
32D VAL* 3.9 9.6 - - + -
33D THR* 1.3 80.2 - - - +
35D LYS* 1.3 62.2 + - - +
119D ILE 4.0 0.2 - - - +
120D LEU* 3.3 5.0 - - - -
121D VAL* 2.7 47.4 + - + +
125D TRP* 3.1 16.3 + - - -
128D THR* 3.3 39.7 - - - -
129D ILE* 4.0 9.8 - - - -
132D GLU* 5.4 4.3 - - + -
233D GLU* 2.2 38.7 + - + -
378D ILE* 3.8 23.6 - - + -
379D LYS* 3.4 11.7 - - - -
380D LEU* 3.6 34.3 - - + -
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Residues in contact with LYS 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D TYR* 1.3 76.2 - - - +
36D TYR* 1.3 72.2 + - - +
37D THR* 3.0 33.3 + - - +
119D ILE 3.6 4.0 - - - +
120D LEU* 3.8 16.8 - - + -
377D VAL* 3.8 0.5 - - - +
378D ILE* 3.3 4.3 - - - -
379D LYS* 2.8 35.4 + - - +
381D LEU* 4.2 34.5 - - + +
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Residues in contact with TYR 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LYS* 1.3 91.0 + - - +
37D THR* 1.3 61.4 + - - +
38D ASN* 3.4 28.6 + - + +
45D PHE* 3.7 22.7 - - - -
117D LEU* 3.5 46.4 + - + +
118D LYS* 4.8 0.7 - - - -
119D ILE* 2.9 36.5 + - + +
136D LEU* 4.9 0.7 - - + -
139D ILE* 3.8 28.9 - - + -
376D ILE* 3.5 30.2 - - + +
377D VAL 3.4 12.8 - - - -
378D ILE* 4.0 14.4 - - + +
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Residues in contact with THR 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LYS* 3.0 28.0 + - - +
36D TYR* 1.3 75.3 + - - +
38D ASN* 1.3 70.4 + - - +
39D ARG* 3.7 14.4 + - + +
376D ILE* 3.4 3.1 - - - +
377D VAL* 2.9 47.5 + - - +
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Residues in contact with ASN 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D TYR* 3.4 27.0 + - + +
37D THR* 1.3 75.4 - - - +
39D ARG* 1.3 62.1 + - - +
40D SER* 2.8 34.8 + - - -
41D SER* 3.7 17.8 - - - +
43D LEU 3.0 27.7 + - - -
45D PHE* 4.6 4.6 - - - -
374D LEU* 4.0 7.0 - - - +
375D ASN 3.7 1.9 - - - +
376D ILE* 3.7 14.5 - - + +
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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