Contacts of the strand formed by residues 111 - 124 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A SER 5.1 1.2 + - - -
42A GLN* 2.9 44.7 + - - +
44A THR* 4.9 7.9 - - + +
108A ILE* 2.8 40.9 + - + +
109A GLU 4.4 1.6 - - - +
110A GLY* 1.3 83.2 - - - +
112A PRO* 1.4 70.6 - - - +
114A HIS* 3.0 30.0 + - + +
31B THR* 4.4 1.8 - - - +
382B GLU* 4.4 4.2 + - - -
384B ASN* 3.5 17.7 - - - +
385B GLY* 3.7 10.3 - - - +
503B EDO 3.0 33.5 + - - +
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Residues in contact with PRO 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLU* 3.3 18.4 - - + +
108A ILE 3.9 1.3 - - - +
110A GLY* 3.5 10.1 - - - +
111A LYS* 1.4 91.5 - - - +
113A THR* 1.3 77.6 + - + +
114A HIS* 3.3 5.9 + - - -
241B ILE 5.8 4.3 - - - +
384B ASN* 4.7 11.5 - - + +
386B ASN* 4.4 5.5 + - - +
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Residues in contact with THR 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE 4.0 3.3 - - - +
46A ASN* 4.3 9.9 - - - +
47A LYS 5.1 0.3 + - - -
107A GLU* 2.7 18.0 + - - +
112A PRO* 1.3 81.5 + - + +
114A HIS* 1.3 75.2 + - - +
115A TYR* 3.6 22.1 - - - -
243B GLU* 4.8 4.1 + - - +
386B ASN* 3.9 5.0 + - - -
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Residues in contact with HIS 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A THR* 3.4 27.2 + - + +
45A PHE 3.5 5.0 + - - -
46A ASN* 5.9 1.4 - - + +
107A GLU* 3.4 5.0 - - - +
108A ILE* 2.8 28.9 + - + -
111A LYS* 3.0 20.0 + - + +
112A PRO 3.3 15.3 - - - -
113A THR* 1.3 89.7 + - - +
115A TYR* 1.3 61.8 + - - +
243B GLU* 5.4 1.3 - - - -
384B ASN 3.7 12.3 - - - -
385B GLY* 3.1 24.8 + - - -
386B ASN* 2.6 28.5 + - - -
387B HIS* 6.2 3.6 - + - -
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Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A THR* 3.8 5.7 - - - -
45A PHE* 2.8 48.4 + - - +
46A ASN* 4.3 3.8 - - - -
47A LYS* 3.8 29.4 - - + +
50A ILE* 3.5 26.7 - - + -
105A SER* 4.0 16.4 - - - -
106A GLU* 3.2 7.0 - - - +
107A GLU* 3.4 48.5 + - + -
108A ILE* 3.7 5.6 - - - -
113A THR* 3.6 23.6 - - - -
114A HIS* 1.3 78.1 - - - +
116A LYS* 1.3 63.9 + - - +
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Residues in contact with LYS 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A THR* 6.0 0.2 - - - +
105A SER* 3.2 5.9 - - - -
106A GLU* 2.9 55.5 + - + +
108A ILE* 3.7 17.5 - - + +
115A TYR* 1.3 73.9 - - - +
117A LEU* 1.3 67.7 + - - +
118A LYS* 5.4 0.6 - - + +
501A CL 3.8 11.2 - - + -
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TYR* 3.5 36.0 - - + +
45A PHE* 3.7 44.0 - - + -
50A ILE* 3.8 31.0 - - + -
53A LEU* 4.0 19.3 - - + -
103A PHE* 4.0 20.0 - - + -
104A THR 3.7 2.7 - - - -
105A SER* 4.5 0.9 - - - -
116A LYS* 1.3 83.5 - - - +
118A LYS* 1.3 59.8 + - - +
119A ILE* 4.4 8.5 - - + -
139A ILE* 4.1 7.4 - - + -
501A CL 3.2 6.8 - - + +
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Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TYR* 4.9 0.7 - - - -
102A SER* 3.5 3.1 - - - +
103A PHE* 3.3 3.8 - - - -
104A THR* 2.8 56.8 + - - +
105A SER* 5.4 1.6 - - - -
106A GLU* 6.4 1.6 - - + -
116A LYS* 4.0 0.8 + - + +
117A LEU* 1.3 73.9 - - - +
119A ILE* 1.3 66.9 + - - +
120A LEU* 4.7 21.1 - - + +
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LYS* 3.7 3.8 - - - +
36A TYR* 3.1 47.7 + - + +
57A PHE* 4.1 12.8 - - + -
101A ILE* 4.0 22.9 - - + -
102A SER 3.3 2.0 - - - -
103A PHE* 3.4 27.6 - - + -
117A LEU* 4.1 8.4 - - + -
118A LYS* 1.3 81.1 - - - +
120A LEU* 1.3 66.8 + - - +
121A VAL* 4.2 15.7 - - + +
135A LEU* 4.5 8.7 - - + -
139A ILE* 3.7 29.6 - - + -
378A ILE* 5.3 3.4 - - + -
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A THR* 4.0 17.5 - - + -
34A TYR 3.4 13.7 - - - +
35A LYS* 3.8 23.8 - - + -
100A GLN 3.4 1.6 - - - +
101A ILE* 3.5 1.7 - - - -
102A SER* 2.8 50.4 + - - +
118A LYS* 4.3 22.4 - - + -
119A ILE* 1.3 76.7 - - - +
121A VAL* 1.3 63.3 + - - +
122A SER* 4.1 3.1 - - - -
381A LEU* 4.8 6.3 - - + -
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A VAL 3.9 0.3 - - - +
33A THR* 3.2 2.1 - - - -
34A TYR* 2.8 54.9 + - + +
100A GLN* 3.2 10.1 - - + +
101A ILE* 4.5 4.9 - - + -
119A ILE* 4.2 9.6 - - + +
120A LEU* 1.3 76.8 - - - +
122A SER* 1.3 60.9 + - - +
128A THR* 4.2 15.0 - - + +
131A TYR* 3.5 38.6 - - + -
135A LEU* 3.8 27.8 - - + -
378A ILE* 5.0 7.0 - - + -
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Residues in contact with SER 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR* 6.0 0.3 - - - -
32A VAL 3.1 6.4 + - - -
33A THR* 2.9 29.6 + - - -
99A GLU 4.3 2.8 - - - +
100A GLN* 3.0 31.9 + - - +
120A LEU* 5.3 3.6 - - - -
121A VAL* 1.3 77.0 - - - +
123A GLY* 1.3 61.4 + - - +
128A THR* 3.6 5.8 - - - -
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Residues in contact with GLY 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR* 4.1 9.8 - - - -
32A VAL* 2.8 32.8 + - - +
100A GLN* 3.9 8.3 - - - -
122A SER* 1.3 78.5 + - - +
124A SER* 1.3 66.2 + - - +
128A THR* 3.5 5.5 - - - +
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Residues in contact with SER 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO 2.9 27.7 + - - -
29A ASP* 4.1 4.6 - - - -
30A VAL 3.4 11.1 + - - -
31A THR* 4.2 6.7 - - - +
123A GLY* 1.3 71.5 - - - -
125A TRP* 1.3 68.6 + - - +
126A LYS* 3.5 12.9 + - - +
127A ASP* 3.0 34.9 + - - +
128A THR* 3.1 13.2 + - - +
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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