Contacts of the strand formed by residues 111 - 124 (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 LYS 111 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D SER 4.8 0.8 + - - -
42D GLN* 3.1 34.2 + - - +
44D THR* 3.8 20.0 + - + +
108D ILE* 3.0 30.7 + - + +
109D GLU 3.3 0.9 - - - +
110D GLY* 1.3 82.8 - - - +
112D PRO* 1.4 70.1 - - - +
113D THR 3.3 0.2 + - - -
114D HIS* 2.9 41.1 + - + +
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Residues in contact with PRO 112 (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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107D GLU* 3.5 14.1 - - - +
108D ILE 4.0 1.5 - - - +
110D GLY* 3.4 10.8 - - - +
111D LYS* 1.4 90.1 - - - +
113D THR* 1.3 77.6 + - + +
114D HIS* 3.4 8.1 + - - -
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Residues in contact with THR 113 (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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45D PHE 4.0 3.6 - - - +
46D ASN* 4.3 10.0 - - - +
47D LYS* 5.0 0.9 + - - +
107D GLU* 2.8 19.3 + - - +
112D PRO* 1.3 81.2 + - + +
114D HIS* 1.3 72.4 + - - +
115D TYR* 3.6 21.3 - - - -
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Residues in contact with HIS 114 (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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44D THR* 3.2 31.4 + - + +
45D PHE 3.5 6.2 + - - -
46D ASN* 5.8 2.3 - - + +
107D GLU* 3.4 4.0 - - - +
108D ILE* 2.8 33.3 + - + +
111D LYS* 2.9 32.5 + - + +
112D PRO 3.4 15.3 - - - -
113D THR* 1.3 89.0 + - - +
115D TYR* 1.3 59.4 + - - +
147D VAL* 6.1 3.2 - - + +
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Residues in contact with TYR 115 (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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44D THR* 3.7 5.5 - - - -
45D PHE* 2.8 44.8 + - - +
46D ASN* 4.3 3.8 - - - -
47D LYS* 3.3 46.6 + - + -
50D ILE* 3.6 28.3 - - + -
105D SER* 4.0 15.0 - - - -
106D GLU 3.4 7.0 - - - +
107D GLU* 3.4 47.9 + - + -
108D ILE* 3.5 6.7 - - - -
113D THR* 3.6 26.6 - - - -
114D HIS* 1.3 74.1 - - - +
116D LYS* 1.3 62.9 + - - +
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Residues in contact with LYS 116 (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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44D THR* 5.8 0.2 - - - +
45D PHE* 5.2 1.3 - - - -
105D SER* 3.2 4.3 - - - -
106D GLU* 2.9 72.4 + - + +
107D GLU 3.9 9.9 + - - -
108D ILE* 3.6 24.3 - - + +
109D GLU 4.9 2.6 - - - +
115D TYR* 1.3 74.5 - - - +
117D LEU* 1.3 67.4 + - - +
118D LYS* 4.8 7.0 - - + +
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Residues in contact with LEU 117 (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* 3.5 33.6 + - + +
45D PHE* 3.7 47.9 - - + -
50D ILE* 3.6 33.2 - - + -
53D LEU* 3.9 20.0 - - + -
103D PHE* 4.0 20.9 - - + -
104D THR 3.7 2.9 - - - -
105D SER* 4.4 1.1 - - - -
116D LYS* 1.3 81.4 - - - +
118D LYS* 1.3 64.8 + - - +
119D ILE* 4.5 8.1 - - + -
139D ILE* 4.0 10.3 - - + -
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Residues in contact with LYS 118 (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* 4.8 1.3 - - - -
102D SER 3.4 2.5 - - - +
103D PHE* 3.4 1.0 - - - -
104D THR* 2.8 57.1 + - - +
105D SER 4.9 4.9 + - - -
106D GLU* 3.9 35.1 + - + +
116D LYS* 4.8 8.5 - - + +
117D LEU* 1.3 78.0 - - - +
119D ILE* 1.3 63.6 + - - +
120D LEU* 5.9 0.9 - - + -
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Residues in contact with ILE 119 (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* 3.6 4.7 - - - +
36D TYR* 2.9 51.9 + - + +
57D PHE* 3.9 18.8 - - + -
101D ILE* 4.3 16.2 - - + -
102D SER 3.3 2.7 - - - -
103D PHE* 3.5 20.6 - - + -
117D LEU* 4.2 6.7 - - + -
118D LYS* 1.3 82.4 - - - +
120D LEU* 1.3 65.2 + - - +
121D VAL* 4.2 20.1 - - + +
135D LEU* 4.5 9.9 - - + -
139D ILE* 3.6 31.4 - - + -
378D ILE* 5.1 2.7 - - + -
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Residues in contact with LEU 120 (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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33D THR* 3.8 25.1 - - + -
34D TYR 3.3 5.6 - - - +
35D LYS* 3.8 25.6 - - + -
100D GLN 3.5 1.4 - - - +
101D ILE* 3.7 2.1 - - - +
102D SER* 2.8 48.8 + - - +
118D LYS 4.3 0.9 - - - -
119D ILE* 1.3 76.1 - - - +
121D VAL* 1.3 62.0 + - - +
122D SER* 4.1 5.6 + - - +
381D LEU* 4.3 8.1 - - + -
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Residues in contact with VAL 121 (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 4.0 0.3 - - - +
33D THR* 3.2 2.3 - - - -
34D TYR* 2.7 57.2 + - + +
100D GLN* 3.3 9.9 - - + +
101D ILE* 4.5 5.6 - - + -
119D ILE* 4.2 10.5 - - + +
120D LEU* 1.3 76.5 - - - +
122D SER* 1.3 62.5 + - - +
128D THR* 4.0 18.1 - - + +
131D TYR* 3.6 36.8 - - + -
135D LEU* 3.8 27.6 - - + -
378D ILE* 5.0 6.5 - - + -
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Residues in contact with SER 122 (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 3.3 9.4 - - - -
33D THR* 3.2 24.7 + - - +
99D GLU 4.4 2.1 - - - +
100D GLN* 3.0 35.0 + - - +
120D LEU* 4.4 6.4 - - - +
121D VAL* 1.3 77.8 + - - +
123D GLY* 1.3 59.2 + - - +
128D THR* 3.4 7.0 - - - +
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Residues in contact with GLY 123 (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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31D THR* 3.2 10.7 - - - -
32D VAL* 2.8 33.1 + - - +
100D GLN* 4.3 6.3 - - - -
122D SER* 1.3 76.6 - - - +
124D SER* 1.3 66.2 + - - -
128D THR* 3.4 3.9 - - - +
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Residues in contact with SER 124 (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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28D PRO 3.1 24.8 + - - -
29D ASP* 4.6 2.3 - - - -
30D VAL 3.4 8.9 + - - -
31D THR* 4.2 8.1 - - - +
123D GLY* 1.3 73.7 - - - -
125D TRP* 1.3 66.9 + - - +
126D LYS* 3.1 14.0 + - - +
127D ASP* 3.0 39.4 + - - +
128D THR* 3.1 12.0 + - - +
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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