Contacts of the strand formed by residues 101 - 112 (chain L) in PDB entry 1CBV
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 LEU 101 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37H VAL* 4.4 3.4 - - + -
46H GLU* 5.7 0.7 - - - -
47H TRP* 3.7 36.0 + - + +
108H PHE* 3.6 54.1 - - + -
41L TYR* 5.6 0.2 - - - +
94L SER* 3.9 24.0 - - - +
95L GLN* 3.1 29.5 - - - +
96L SER* 4.5 1.8 - - - +
98L HIS 3.8 1.4 + - - -
99L VAL* 4.4 1.0 - - - +
100L PRO* 1.3 75.9 - - - +
102L THR* 1.3 59.9 + - - +
103L PHE* 3.5 33.8 - - + -
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Residues in contact with THR 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1L ASP 3.4 17.7 + - - +
2L VAL 3.0 24.0 + - - +
3L VAL* 4.5 2.2 - - + -
4L MET* 3.7 14.3 - - - +
94L SER* 3.4 1.6 - - - -
95L GLN* 2.9 38.0 + - - +
100L PRO* 3.0 16.4 + - - +
101L LEU* 1.3 74.8 + - - +
103L PHE* 1.3 77.5 - - - +
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Residues in contact with PHE 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H VAL* 4.5 6.1 - - + -
45H LEU* 3.3 60.2 + - + +
46H GLU* 4.7 1.8 - - - -
47H TRP 4.7 3.6 - - - -
108H PHE* 5.9 0.2 - + - -
111H TRP* 3.5 34.3 - + - -
4L MET* 3.8 9.3 + - - +
41L TYR* 4.2 9.2 - + - -
92L PHE* 4.6 8.7 - - + -
93L CYS 3.1 9.0 - - - +
94L SER* 3.7 21.1 - - - -
101L LEU* 3.5 37.5 - - + -
102L THR* 1.3 95.6 - - - +
104L GLY* 1.3 71.7 - - - +
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Residues in contact with GLY 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H GLY* 5.7 1.0 - - - -
45H LEU 5.4 2.4 + - - -
4L MET* 3.2 25.0 - - - +
6L GLN* 3.3 15.7 + - - -
92L PHE* 3.3 15.4 - - - -
93L CYS 2.7 14.3 + - - +
103L PHE* 1.3 79.3 - - - +
105L ALA* 1.3 63.1 + - - -
106L GLY 3.1 4.2 + - - -
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Residues in contact with ALA 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H LYS* 3.5 38.5 + - - +
44H GLY* 5.6 2.9 - - - -
4L MET 3.9 6.5 + - - +
6L GLN* 3.7 3.6 + - + +
9L LEU* 4.1 27.6 - - + -
90L VAL* 4.9 1.0 - - - +
92L PHE* 4.0 8.6 - - - -
104L GLY* 1.3 71.1 - - - -
106L GLY* 1.3 60.4 + - - +
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Residues in contact with GLY 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L GLN* 3.0 11.8 + - - +
9L LEU* 3.9 21.9 - - - +
90L VAL* 3.5 16.3 - - - +
91L TYR 3.1 15.5 - - - -
92L PHE* 3.8 6.5 - - - -
104L GLY 3.1 1.4 - - - -
105L ALA* 1.3 83.7 - - - +
107L THR* 1.3 63.3 + - - -
108L LYS 4.2 0.2 + - - -
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Residues in contact with THR 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L GLN* 3.0 21.0 + - - +
8L PRO* 2.7 36.0 + - + +
9L LEU 3.7 1.6 - - - -
11L LEU* 4.4 12.3 - - + -
21L ILE* 3.3 42.1 - - + +
89L GLY 3.7 1.4 - - - +
90L VAL* 3.2 4.1 - - - +
91L TYR* 2.8 35.1 + - - +
106L GLY* 1.3 73.1 - - - -
108L LYS* 1.3 61.2 + - - +
109L LEU* 3.9 2.0 + - + -
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Residues in contact with LYS 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L LEU 3.2 14.3 + - - +
10L SER* 3.7 3.6 - - - -
11L LEU 3.0 25.3 + - - -
45L PRO* 5.8 6.1 - - - +
89L GLY* 3.4 17.1 - - - +
90L VAL* 4.1 19.4 - - + +
106L GLY 4.2 0.4 - - - -
107L THR* 1.3 72.9 - - - +
109L LEU* 1.3 67.8 + - - +
110L GLU* 3.2 9.1 + - + +
147L LYS* 5.7 5.4 - - - +
170L ASP* 2.8 36.6 + - - +
171L GLN 6.0 0.2 - - - +
178L TYR* 5.0 9.2 - - - -
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Residues in contact with LEU 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L LEU* 3.3 38.4 - - + +
13L VAL* 4.8 3.6 - - + -
19L ALA* 4.2 5.4 - - + -
21L ILE* 3.8 20.6 - - + -
80L ILE* 4.2 11.2 - - + -
83L VAL* 4.2 22.2 - - + -
87L ASP 3.7 11.7 - - - +
88L LEU* 3.4 28.9 - - + +
89L GLY 3.2 11.7 + - - +
91L TYR* 3.4 32.3 - - + -
107L THR* 3.9 2.1 + - + -
108L LYS* 1.3 73.1 - - - +
110L GLU* 1.3 62.1 + - - +
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Residues in contact with GLU 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L SER* 3.3 17.0 + - - -
11L LEU 2.8 14.9 + - - +
12L PRO* 3.0 35.8 - - + +
13L VAL* 3.2 18.4 + - - +
88L LEU* 4.3 3.6 - - - +
108L LYS* 3.2 12.4 + - + +
109L LEU* 1.3 76.7 - - - +
111L LEU* 1.3 61.8 - - - +
145L TYR* 3.0 31.7 + - - +
146L PRO* 5.2 1.6 - - - +
147L LYS* 5.2 6.3 + - - +
171L GLN* 3.6 10.8 - - - +
178L TYR* 3.6 24.8 + - - +
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Residues in contact with LEU 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L VAL* 3.2 19.7 - - + +
14L SER* 4.7 1.1 - - - -
15L LEU* 4.4 35.2 - - + +
85L ALA* 5.6 2.5 - - + -
88L LEU* 3.8 24.7 - - + -
110L GLU* 1.3 75.3 - - - +
112L LYS* 1.4 73.5 + - - +
113L ARG* 4.6 0.7 - - - +
145L TYR* 3.0 10.9 + - - -
171L GLN* 2.5 43.2 + - - +
176L SER* 4.6 9.9 - - - +
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Residues in contact with LYS 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L PRO* 4.2 21.9 - - + +
13L VAL 3.1 20.0 + - - +
14L SER* 4.1 21.2 + - - +
111L LEU* 1.4 81.2 - - - +
113L ARG* 1.3 70.0 + - - +
115L ASP* 5.6 3.2 + - - -
145L TYR* 3.9 21.9 + - - +
146L PRO* 6.0 1.4 - - - +
176L SER* 5.2 0.9 + - - -
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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