Contacts of the strand formed by residues 113 - 120 (chain H) in PDB entry 3T30
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 VAL 113 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H CYS 3.8 0.3 - - - +
22H GLU* 3.4 2.0 - - - -
23H LEU* 2.7 45.7 + - + +
49H ILE* 3.4 30.7 - - + -
50H CYS 3.5 11.0 - - - +
51H LEU* 3.7 10.8 - - + -
60H HIS* 3.5 33.4 - - + -
62H VAL* 4.2 10.8 - - + -
83H LEU* 4.6 1.8 - - + -
106H LEU* 3.7 20.0 - - + -
111H GLY* 4.0 2.2 - - - -
112H PRO* 1.3 78.9 - - - +
114H PHE* 1.3 66.2 + - - +
115H LEU* 4.7 1.8 - - + -
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Residues in contact with PHE 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H CYS 3.3 7.9 - - - +
22H GLU* 3.5 46.2 - - + -
49H ILE* 3.2 9.0 - - - +
50H CYS* 2.9 42.9 + - + +
52H GLY* 3.6 27.1 - - - -
112H PRO* 4.0 11.7 - - + -
113H VAL* 1.3 73.5 - - - +
115H LEU* 1.3 65.7 + - - +
61I ARG* 3.4 38.8 - - - -
63I GLU* 5.7 0.4 - - - -
79I THR* 3.6 35.4 - - + +
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Residues in contact with LEU 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H TRP* 3.8 16.8 - - + -
20H GLY* 3.1 4.2 - - - -
21H CYS* 2.9 39.4 + - - +
23H LEU* 3.8 29.2 - - + -
46H LEU* 4.0 6.7 - - + -
48H THR 3.4 5.8 - - - +
49H ILE* 3.7 33.4 - - + -
62H VAL* 4.6 4.7 - - + -
104H PHE* 3.6 40.6 - - + -
113H VAL* 4.3 4.5 - - + +
114H PHE* 1.3 83.3 - - - +
116H SER* 1.3 61.9 + - - +
78I VAL* 4.7 1.0 - - - +
79I THR 4.6 2.9 + - - +
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Residues in contact with SER 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H LEU* 6.1 0.7 - - - -
19H TRP* 3.5 13.0 - - - -
46H LEU* 3.7 7.1 - - - +
47H HIS* 2.8 26.4 + - - +
48H THR* 2.9 35.1 + - - +
115H LEU* 1.3 72.0 - - - +
117H GLY* 1.3 59.7 + - - +
78I VAL* 3.3 17.7 - - - -
79I THR 3.2 23.5 + - - -
80I ILE* 4.2 8.6 - - - +
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Residues in contact with GLY 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H LEU* 3.4 7.7 - - - +
19H TRP* 2.8 34.7 + - - +
45H LEU 3.0 14.4 - - - -
47H HIS* 3.6 14.8 - - - -
116H SER* 1.3 79.0 - - - +
118H GLN* 1.3 69.2 + - - +
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Residues in contact with GLN 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H THR* 5.0 15.4 + - - +
17H VAL 3.2 12.6 - - - +
18H LEU* 3.8 17.9 - - + +
19H TRP* 4.2 3.1 - - - +
44H LEU* 3.7 2.6 - - - -
45H LEU* 2.8 51.8 + - + +
47H HIS* 3.0 29.3 + - + -
117H GLY* 1.3 79.7 - - - +
119H GLU* 1.3 66.9 + - - +
120H ARG* 5.9 0.4 - - + -
97I GLN* 2.8 31.2 + - - +
98I LEU* 3.8 12.6 - - - +
99I SER 5.1 1.0 + - - -
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Residues in contact with GLU 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H THR 3.5 1.3 - - - +
16H THR* 3.1 7.3 - - - -
17H VAL* 2.8 60.4 + - + +
18H LEU 4.6 0.5 - - - +
19H TRP* 4.0 28.5 - - + +
32H PHE* 3.5 37.9 - - + -
34H PRO* 5.4 2.9 - - - +
42H CYS* 4.5 4.9 - - - -
43H ARG 3.6 5.8 - - - +
44H LEU* 4.7 2.7 - - + +
118H GLN* 1.3 73.3 - - - +
120H ARG* 1.3 58.5 + - - +
121H TYR* 4.6 8.3 - - + -
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Residues in contact with ARG 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H THR* 3.1 7.1 + - - +
16H THR* 3.8 23.1 - - + -
41H SER* 4.1 4.3 + - - +
42H CYS* 3.3 2.6 - - - -
43H ARG* 2.9 48.2 + - + +
45H LEU* 4.5 28.9 - - + -
97H GLN* 5.1 6.7 + - - -
118H GLN* 3.8 0.4 + - + -
119H GLU* 1.3 75.1 - - - +
121H TYR* 1.3 72.8 + - - +
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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