Contacts of the helix formed by residues 46 - 60 (chain C) 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 ASN 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C PHE* 1.3 74.1 - - - +
47C LYS* 1.3 64.1 + - - +
48C GLU* 3.4 12.1 + - + +
49C ALA* 2.9 35.2 + - - +
50C ILE* 3.1 27.0 + - - +
113C THR* 3.8 14.6 - - - +
114C HIS* 5.8 3.6 - - + +
115C TYR* 4.2 0.7 - - - -
146C PHE* 3.0 27.5 + - - +
147C VAL* 3.9 15.1 - - + +
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Residues in contact with LYS 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ASN* 1.3 74.9 - - - +
48C GLU* 1.3 57.8 + - + +
50C ILE* 3.7 9.6 - - - +
51C ASN* 2.9 46.3 + - - +
113C THR 4.6 0.4 + - - -
115C TYR* 4.1 19.9 - - + +
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Residues in contact with GLU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ASN* 3.2 13.1 + - - +
47C LYS* 1.3 78.4 - - + +
49C ALA* 1.3 63.5 + - - +
51C ASN* 4.0 5.2 - - - +
52C TRP* 3.1 25.1 + - - +
146C PHE* 3.9 25.4 - - + +
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Residues in contact with ALA 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C PHE* 3.9 24.2 - - + -
46C ASN* 2.9 22.7 + - - +
48C GLU* 1.3 75.3 - - - +
50C ILE* 1.3 58.7 + - - +
52C TRP* 3.3 2.9 + - - +
53C LEU* 2.9 35.9 + - - +
142C ALA* 4.2 9.5 - - + +
146C PHE* 3.9 23.5 - - + +
147C VAL* 4.2 6.7 - - + -
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Residues in contact with ILE 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C PHE* 4.4 4.3 - - + -
46C ASN 3.1 18.5 + - - +
47C LYS* 3.3 8.9 + - - +
49C ALA* 1.3 74.1 - - - +
51C ASN* 1.3 61.7 + - - +
53C LEU* 3.2 9.3 + - + +
54C LYS* 2.9 57.4 + - - +
103C PHE* 3.9 6.2 - - + -
105C SER* 3.7 21.1 - - - +
115C TYR* 3.6 40.2 - - + -
117C LEU* 3.7 21.3 - - + -
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Residues in contact with ASN 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1C HIS* 6.5 0.9 - - + -
47C LYS* 2.9 31.0 + - - +
48C GLU* 4.1 5.0 - - - +
50C ILE* 1.3 80.6 - - - +
52C TRP* 1.3 60.9 + - - +
54C LYS* 3.3 20.2 + - - +
55C GLU* 3.2 21.3 + - - +
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Residues in contact with TRP 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C SER* 3.6 32.9 - - - -
3C GLU 5.0 0.6 + - - -
5C VAL* 3.5 32.3 - - + -
48C GLU 3.1 18.8 + - - +
49C ALA 3.6 1.6 - - - +
51C ASN* 1.3 74.3 - - - +
53C LEU* 1.3 64.3 + - + +
55C GLU* 3.1 9.1 + - - +
56C GLN* 2.9 53.0 + - + +
138C LEU* 3.6 19.3 - - + -
141C GLU* 4.1 14.8 - - + -
142C ALA* 3.5 35.9 - - + -
145C LYS* 4.0 20.3 - - + +
146C PHE* 3.4 27.6 - + + -
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C PHE* 4.4 7.9 - - + -
49C ALA 2.9 25.0 + - - +
50C ILE* 3.2 5.6 + - - +
52C TRP* 1.3 78.6 - - + +
54C LYS* 1.3 60.0 + - - +
56C GLN* 4.3 1.6 - - + -
57C PHE* 2.8 60.0 + - + -
103C PHE* 3.8 15.3 - - + -
117C LEU* 4.1 27.1 - - + -
138C LEU* 3.6 33.7 - - + +
139C ILE* 3.8 8.5 - - + +
142C ALA* 3.7 16.4 - - + -
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Residues in contact with LYS 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ILE* 2.9 37.5 + - - +
51C ASN* 3.3 20.6 + - - +
53C LEU* 1.3 71.0 - - - +
55C GLU* 1.3 63.5 + - - +
57C PHE* 3.9 3.6 - - - +
58C SER* 3.2 22.2 + - - -
103C PHE* 3.5 48.5 + - + -
104C THR* 4.9 4.4 - - - +
105C SER* 5.2 2.5 + - - -
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Residues in contact with GLU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1C HIS* 2.8 34.6 + - + -
1C MSE 3.8 11.9 - - + +
2C SER* 2.7 34.2 + - - +
51C ASN 3.2 9.3 + - - +
52C TRP* 3.1 11.0 + - - +
53C LEU 3.1 0.6 - - - -
54C LYS* 1.3 81.0 - - - +
56C GLN* 1.3 61.5 + - - +
58C SER* 2.6 25.2 + - - +
59C TYR* 3.1 42.1 + - + +
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Residues in contact with GLN 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C SER* 2.8 25.3 + - - -
3C GLU 3.0 19.8 + - - -
4C PRO* 3.6 2.6 - - - +
5C VAL* 2.9 27.8 + - - +
6C ILE 4.4 1.0 + - - -
52C TRP* 2.9 57.5 + - + +
53C LEU* 3.8 5.8 - - - +
55C GLU* 1.3 75.0 - - - +
57C PHE* 1.3 65.2 + - + +
59C TYR* 3.2 27.4 + - - +
60C LEU* 3.4 11.8 + - - +
138C LEU* 3.7 21.6 - - + +
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Residues in contact with PHE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C LEU* 2.8 49.5 + - + +
54C LYS* 3.9 4.0 - - - +
56C GLN* 1.3 71.5 - - - +
58C SER* 1.3 62.5 + - - +
60C LEU* 3.2 24.5 + - - +
97C PRO* 3.5 13.1 - - + +
101C ILE* 4.1 26.9 - - + -
103C PHE* 3.5 39.7 - + + -
119C ILE* 4.0 14.6 - - + -
135C LEU* 3.6 28.5 - - + -
138C LEU* 4.0 17.5 - - + -
139C ILE* 4.1 16.2 - - + -
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Residues in contact with SER 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LYS 3.2 11.7 + - - -
55C GLU* 2.6 23.1 + - - +
57C PHE* 1.3 78.8 - - - +
59C TYR* 1.3 70.3 + - - +
61C GLY* 3.1 16.5 + - - -
62C ASN* 4.2 4.6 + - - +
97C PRO* 4.0 8.9 - - - +
98C GLU* 6.2 4.9 - - - -
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Residues in contact with TYR 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MSE 3.5 28.6 - - + +
2C SER* 2.8 34.1 + - - -
4C PRO* 3.6 36.1 - - + -
6C ILE 5.7 3.1 - - - +
55C GLU* 3.1 42.6 + - + -
56C GLN* 3.2 30.4 + - - +
58C SER* 1.3 82.9 + - - +
60C LEU* 1.3 66.1 + - + +
61C GLY 3.1 0.2 - - - -
62C ASN* 2.9 39.2 + - + +
63C LEU* 3.8 8.1 + - - +
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 4.0 28.9 - - + +
56C GLN 3.8 9.2 - - - +
57C PHE* 3.3 18.6 - - - +
58C SER 3.2 0.6 - - - -
59C TYR* 1.3 78.4 - - + +
61C GLY* 1.3 57.8 + - - +
62C ASN 3.3 1.0 + - - -
63C LEU* 3.3 39.5 + - + +
95C LEU* 3.8 27.5 - - + +
97C PRO* 4.6 4.0 - - + -
101C ILE* 4.8 0.7 - - + -
131C TYR* 4.1 17.5 - - + -
134C PRO* 4.4 12.8 - - + -
135C LEU* 3.7 30.1 - - + -
138C LEU* 4.5 5.8 - - + -
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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