Contacts of the strand formed by residues 128 - 139 (chain A) in PDB entry 1TVG
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 SER 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A PHE* 3.5 26.6 - - - -
39A TRP* 3.3 5.2 - - - -
40A THR* 2.9 23.2 + - - -
66A SER* 3.0 7.3 - - - -
67A TYR* 2.9 38.4 + - - +
69A VAL* 3.9 1.6 - - - +
126A PHE* 3.8 11.2 - - - -
127A ALA* 1.3 74.2 - - - +
129A VAL* 1.3 66.6 + - - +
130A HIS* 4.1 11.9 - - - -
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Residues in contact with VAL 129 (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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30A ILE* 3.9 26.6 - - + +
38A PHE* 3.3 3.4 - - - +
39A TRP* 2.9 36.1 + - + -
49A PHE* 3.9 20.4 - - + -
64A ILE* 4.9 5.2 - - + -
65A GLN 3.8 6.3 - - - +
66A SER* 4.2 6.5 - - - -
69A VAL* 4.7 2.5 - - + -
72A LEU* 6.0 3.4 - - + -
119A ILE* 4.0 20.0 - - + -
128A SER* 1.3 77.0 - - - +
130A HIS* 1.3 62.3 + - - +
131A SER 4.0 4.9 - - - +
132A VAL* 3.8 28.7 - - + -
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Residues in contact with HIS 130 (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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29A ASN 3.2 5.1 - - - +
30A ILE* 4.5 0.4 - - - -
34A ASN 4.0 0.3 - - - +
35A PRO 2.8 25.1 - - - +
36A GLU* 4.2 5.9 + - - -
37A THR 3.3 5.8 - - - +
38A PHE* 3.5 40.4 - + + +
65A GLN* 2.7 32.0 + - + +
66A SER* 4.3 10.1 - - - -
67A TYR* 4.5 6.1 - + + -
100A LEU* 3.8 34.6 - - + +
128A SER* 4.3 11.3 - - - -
129A VAL* 1.3 74.8 - - - +
131A SER* 1.3 59.4 + - - +
221A CA 2.6 28.4 - - - -
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Residues in contact with SER 131 (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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4A ILE* 4.0 5.5 + - - +
30A ILE* 3.3 11.9 + - - +
33A GLY* 5.5 7.9 + - - -
34A ASN 5.3 5.8 - - - -
35A PRO* 5.5 1.6 - - - -
63A VAL 4.4 0.7 - - - -
64A ILE* 3.5 0.7 - - - +
65A GLN* 2.8 47.7 + - - +
129A VAL* 3.6 1.7 - - - -
130A HIS* 1.3 80.3 - - - +
132A VAL* 1.3 72.9 + - - +
133A SER* 3.7 14.9 + - - -
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Residues in contact with VAL 132 (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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4A ILE 2.9 11.3 + - - -
7A CYS* 3.3 19.3 - - - +
30A ILE* 3.2 33.0 + - + +
31A ILE* 4.3 1.6 - - - +
49A PHE* 4.0 11.2 - - + -
51A ILE* 3.5 14.8 - - + -
62A LEU* 5.6 0.9 - - + -
63A VAL 3.4 5.4 - - - +
64A ILE* 4.2 14.1 - - + -
115A LEU* 5.5 0.4 - - + -
117A PHE* 3.4 35.0 - - + -
129A VAL* 3.8 11.9 - - + -
131A SER* 1.3 78.9 + - - +
133A SER* 1.3 68.0 + - - +
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Residues in contact with SER 133 (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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4A ILE* 2.3 52.5 + - - +
7A CYS* 4.0 2.5 - - - -
62A LEU* 3.2 9.4 - - - +
63A VAL* 2.8 52.1 + - - +
131A SER* 3.7 7.6 + - - -
132A VAL* 1.3 74.9 - - - +
134A ALA* 1.3 62.3 + - - +
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Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ILE 3.2 5.1 + - - -
5A ASP* 2.9 24.4 - - - +
6A LEU* 3.0 20.1 + - + +
7A CYS* 3.5 21.0 - - - -
53A PHE* 4.5 0.9 - - + -
59A ILE* 4.3 17.9 - - + -
61A ARG 3.2 4.7 - - - +
62A LEU* 3.7 17.0 - - + -
133A SER* 1.3 77.3 - - - +
135A GLU* 1.3 60.6 + - - +
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Residues in contact with GLU 135 (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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5A ASP* 3.2 11.9 - - + +
6A LEU* 4.0 2.0 - - - -
59A ILE* 3.5 4.7 - - - +
60A GLU* 2.8 42.3 + - + +
61A ARG* 2.8 55.4 + - + +
134A ALA* 1.3 73.5 - - - +
136A GLY* 1.3 61.2 + - - +
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Residues in contact with GLY 136 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ASP* 3.4 11.1 + - - +
6A LEU* 3.7 12.0 - - - +
58A ARG 3.1 13.0 - - - -
60A GLU* 4.4 8.7 - - - -
135A GLU* 1.3 80.8 - - - +
137A THR* 1.3 65.8 + - - -
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Residues in contact with THR 137 (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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6A LEU* 4.1 4.0 - - - +
57A VAL* 3.3 3.4 - - - +
58A ARG* 2.8 39.5 + - - +
136A GLY* 1.3 76.8 + - - -
138A VAL* 1.3 76.7 + - - +
139A VAL* 4.2 1.5 - - + +
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Residues in contact with VAL 138 (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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6A LEU* 4.0 17.9 - - + -
55A LYS* 3.5 41.5 - - + -
56A HIS 3.5 9.0 - - - +
57A VAL* 4.3 1.6 - - + +
137A THR* 1.3 89.6 - - - +
139A VAL* 1.3 72.0 + - - +
140A SER* 4.2 5.0 + - - +
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Residues in contact with VAL 139 (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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55A LYS* 5.5 0.3 - - - +
56A HIS* 2.7 42.8 + - + +
57A VAL 4.4 1.6 - - - -
58A ARG* 3.6 34.3 - - + +
137A THR* 4.2 5.8 - - + +
138A VAL* 1.3 81.9 - - - +
140A SER* 1.3 71.9 + - - +
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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