Contacts of the strand formed by residues 111 - 124 (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 LYS 111 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C SER 5.0 0.8 + - - -
42C GLN* 3.3 30.9 + - - +
44C THR* 3.8 18.9 + - + +
108C ILE* 2.9 35.3 + - + +
109C GLU 3.3 1.3 - - - +
110C GLY* 1.3 82.2 - - - +
112C PRO* 1.3 69.0 - - - +
113C THR 3.3 0.2 + - - -
114C HIS* 2.9 38.9 + - + +
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Residues in contact with PRO 112 (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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107C GLU* 3.6 11.4 - - + +
108C ILE 4.0 1.3 - - - +
110C GLY* 3.3 12.3 - - - +
111C LYS* 1.3 89.9 - - - +
113C THR* 1.3 77.0 + - + +
114C HIS* 3.4 7.6 - - - -
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Residues in contact with THR 113 (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 3.7 4.2 - - - +
46C ASN* 3.8 13.7 - - - +
47C LYS 4.6 0.3 + - - -
107C GLU* 2.7 21.1 + - - +
112C PRO* 1.3 81.7 + - + +
114C HIS* 1.3 68.9 + - - +
115C TYR* 3.5 21.7 - - - -
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Residues in contact with HIS 114 (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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44C THR* 3.1 30.0 + - - +
45C PHE 3.3 5.6 + - - -
46C ASN* 5.8 3.0 - - + +
107C GLU* 3.4 6.4 - - - +
108C ILE* 2.9 27.8 + - + -
111C LYS* 2.9 32.8 + - + +
112C PRO 3.4 21.7 + - - -
113C THR* 1.3 87.6 + - - +
115C TYR* 1.3 63.2 + - - +
147C VAL* 5.8 6.0 - - + +
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Residues in contact with TYR 115 (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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44C THR* 3.7 6.4 - - - -
45C PHE* 2.8 45.4 + - + +
46C ASN* 4.2 2.2 - - - -
47C LYS* 4.1 21.8 - - + +
50C ILE* 3.6 26.0 - - + -
105C SER* 3.9 17.7 - - - -
106C GLU* 3.3 8.3 - - - +
107C GLU* 3.4 46.5 + - + -
108C ILE* 3.8 6.3 - - - -
113C THR* 3.5 26.8 - - - -
114C HIS* 1.3 77.7 - - - +
116C LYS* 1.3 61.7 + - - +
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Residues in contact with LYS 116 (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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44C THR* 6.0 0.2 - - - -
105C SER* 3.3 4.7 - - - -
106C GLU* 3.0 55.2 + - + +
108C ILE* 3.9 14.7 - - + +
115C TYR* 1.3 74.6 - - - +
117C LEU* 1.3 67.4 + - - +
118C LYS* 5.1 9.0 - - + +
501C CL 3.8 10.8 - - + -
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Residues in contact with LEU 117 (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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36C TYR* 3.6 34.8 - - + +
45C PHE* 3.7 44.0 - - + -
50C ILE* 3.7 33.7 - - + -
53C LEU* 4.1 18.6 - - + -
103C PHE* 3.9 21.8 - - + -
104C THR 3.7 2.5 - - - -
105C SER* 4.3 1.8 - - - -
116C LYS* 1.3 80.7 - - - +
118C LYS* 1.3 66.3 + - - +
119C ILE* 4.6 8.1 - - + -
139C ILE* 4.3 5.2 - - + -
501C CL 3.2 6.9 - - + +
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Residues in contact with LYS 118 (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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36C TYR* 4.8 1.1 - - - -
102C SER 3.6 1.8 - - - +
103C PHE* 3.4 3.6 - - - -
104C THR* 2.8 54.0 + - - +
105C SER* 5.8 0.9 - - - -
106C GLU* 3.8 26.6 + - + +
116C LYS* 5.1 10.5 - - + +
117C LEU* 1.3 79.3 - - - +
119C ILE* 1.3 62.6 + - - +
120C LEU* 5.8 0.9 - - + -
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Residues in contact with ILE 119 (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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35C LYS* 3.7 4.5 - - - +
36C TYR* 3.0 48.6 + - + +
57C PHE* 4.0 17.5 - - + -
101C ILE* 4.1 23.1 - - + -
102C SER 3.3 2.7 - - - +
103C PHE* 3.6 22.2 - - + -
117C LEU* 4.2 6.2 - - + -
118C LYS* 1.3 81.2 - - - +
120C LEU* 1.3 69.8 + - - +
121C VAL* 4.3 13.0 - - + +
135C LEU* 4.6 8.5 - - + -
139C ILE* 3.7 31.2 - - + -
378C ILE* 5.3 2.7 - - + -
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Residues in contact with LEU 120 (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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33C THR* 4.2 17.9 - - + -
34C TYR 3.4 4.7 - - - +
35C LYS* 3.7 39.7 - - + -
100C GLN 3.5 1.0 - - - +
101C ILE* 3.6 2.4 - - - -
102C SER* 2.8 46.4 + - - +
118C LYS* 5.8 0.7 - - + -
119C ILE* 1.3 77.0 - - - +
121C VAL* 1.3 62.2 + - - +
122C SER* 4.2 6.1 - - - +
381C LEU* 4.4 5.8 - - + -
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Residues in contact with VAL 121 (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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32C VAL 4.0 0.2 - - - +
33C THR* 3.2 1.9 - - - -
34C TYR* 2.7 54.9 + - + +
100C GLN* 3.2 9.6 - - + +
101C ILE* 4.6 5.2 - - + -
119C ILE* 4.3 9.9 - - + +
120C LEU* 1.3 76.5 - - - +
122C SER* 1.3 62.6 + - - +
128C THR* 4.0 17.7 - - + +
131C TYR* 3.5 37.0 - - + -
135C LEU* 3.8 27.6 - - + -
378C ILE* 5.0 6.7 - - + -
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Residues in contact with SER 122 (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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32C VAL 3.3 5.6 - - - -
33C THR* 3.3 27.6 + - - +
99C GLU 4.4 2.4 - - - +
100C GLN* 2.9 34.4 + - - +
120C LEU* 4.5 6.8 - - - +
121C VAL* 1.3 79.0 + - - +
123C GLY* 1.3 57.8 + - - +
128C THR* 3.6 5.6 - - - -
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Residues in contact with GLY 123 (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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31C THR* 3.4 8.9 - - - -
32C VAL* 2.9 30.0 + - - +
100C GLN* 4.0 8.5 - - - -
122C SER* 1.3 74.8 - - - +
124C SER* 1.3 68.8 + - - +
128C THR* 3.5 5.5 - - - +
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Residues in contact with SER 124 (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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28C PRO 3.2 24.8 + - - -
29C ASP* 4.7 1.4 - - - -
30C VAL 3.4 11.7 + - - -
31C THR* 4.2 7.0 - - - +
123C GLY* 1.3 74.1 - - - -
125C TRP* 1.3 70.0 + - - +
126C LYS* 3.3 12.7 + - - +
127C ASP* 2.9 38.9 + - - +
128C THR* 3.1 10.7 + - - -
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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