Contacts of the strand formed by residues 43 - 51 (chain I) 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 ARG 43 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H THR* 5.4 5.7 - - - +
16H THR* 4.4 17.5 + - - +
42I CYS* 1.3 89.9 + - - +
44I LEU* 1.3 61.1 + - - +
45I LEU* 3.8 17.4 + - + -
97I GLN* 4.2 26.9 + - - +
98I LEU 3.4 16.6 - - - -
99I SER* 2.6 32.3 + - - +
100I PRO* 4.4 0.4 - - - -
118I GLN 3.6 0.5 - - - +
119I GLU* 3.6 2.9 - - - -
120I ARG* 2.9 41.1 + - + +
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Residues in contact with LEU 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I TRP* 3.8 42.6 - - + -
32I PHE* 3.7 29.0 - - + -
43I ARG* 1.3 70.8 - - - +
45I LEU* 1.3 67.3 + - - +
46I LEU* 3.6 4.4 + - + -
96I VAL 3.8 0.2 - - - +
97I GLN* 3.4 2.4 - - - -
98I LEU* 2.8 50.1 + - + +
100I PRO* 4.8 0.4 - - + +
102I VAL* 4.1 12.6 - - + -
104I PHE* 3.9 33.0 - - + -
118I GLN 3.5 18.4 - - - +
119I GLU* 4.4 3.1 - - + +
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Residues in contact with LEU 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I ARG* 4.3 11.2 - - + -
44I LEU* 1.3 74.3 - - - +
46I LEU* 1.3 59.9 + - - +
47I HIS* 3.5 17.5 + - + +
95I GLY 6.2 0.7 - - - +
96I VAL 3.4 4.5 - - - +
97I GLN* 3.4 40.2 - - + +
117I GLY* 3.0 7.4 - - - -
118I GLN* 2.8 59.6 + - + +
120I ARG* 3.8 42.4 - - + +
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Residues in contact with LEU 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I TRP* 4.2 16.8 - - + -
44I LEU* 3.6 2.8 + - + -
45I LEU* 1.3 68.8 - - - +
47I HIS* 1.3 61.2 + - - +
48I THR 4.7 4.9 - - - +
49I ILE* 4.5 3.4 - - + -
64I ILE* 5.6 0.7 - - + -
80I ILE* 4.0 21.5 - - + -
93I MET* 2.9 56.3 - - + +
94I VAL* 3.9 1.9 + - - -
96I VAL* 3.0 31.2 + - + +
98I LEU* 4.0 20.0 - - + -
104I PHE* 4.3 2.7 - - + -
115I LEU* 4.3 17.0 - - + -
116I SER 3.6 15.3 - - - +
117I GLY* 4.5 0.4 - - - -
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Residues in contact with HIS 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I LEU* 3.5 22.0 + - + +
46I LEU* 1.3 76.9 - - - +
48I THR* 1.3 68.3 + - + +
92I SER* 3.5 1.7 + - - -
93I MET* 2.7 29.3 + - - -
94I VAL* 3.5 19.3 + - + +
95I GLY 5.2 1.3 - - - -
116I SER* 3.0 21.5 + - - +
117I GLY* 3.7 12.3 + - - -
118I GLN* 3.7 39.7 + - + -
95J GLY 5.2 1.4 + - - -
96J VAL* 3.6 45.4 - - + +
98J LEU* 6.0 0.6 - - + +
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Residues in contact with THR 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I LEU* 4.7 0.7 - - - +
47I HIS* 1.3 87.3 - - + +
49I ILE* 1.3 69.8 + - - +
50I CYS* 3.7 4.2 - - - -
90I MET* 3.7 16.2 - - + -
91I VAL 3.3 10.1 - - - +
92I SER* 4.2 7.0 - - - -
93I MET* 4.7 0.4 - - - +
115I LEU* 3.5 2.3 - - - +
116I SER* 2.6 47.1 + - - +
79J THR 3.8 0.2 + - - -
80J ILE* 3.0 32.1 + - + +
93J MET* 3.9 22.9 - - + -
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Residues in contact with ILE 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I LEU* 4.5 5.6 - - + -
48I THR* 1.3 79.4 - - - +
50I CYS* 1.3 62.5 + - - +
62I VAL* 4.3 11.9 - - + -
80I ILE* 3.7 30.3 - - + -
81I ALA* 3.8 19.3 - - + -
83I LEU* 3.5 13.1 - - + +
90I MET* 3.2 3.3 - - - +
91I VAL* 3.0 38.9 + - + -
93I MET* 4.0 18.6 - - + -
113I VAL* 3.5 24.5 - - + -
114I PHE 3.3 6.7 - - - +
115I LEU* 3.9 20.0 - - + -
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Residues in contact with CYS 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I THR* 3.7 7.6 - - - -
49I ILE* 1.3 79.3 - - - +
51I LEU* 1.3 62.6 + - - +
83I LEU* 4.3 0.7 - - - -
89I PRO 3.6 4.9 - - - -
90I MET* 3.7 18.2 - - - -
113I VAL* 3.5 5.7 - - - -
114I PHE* 2.8 34.8 + - - +
79J THR* 3.8 16.4 - - + -
80J ILE 3.7 4.0 - - - -
81J ALA* 3.6 34.1 - - - -
82J SER* 3.4 18.2 - - - +
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Residues in contact with LEU 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I CYS* 1.3 73.0 - - - +
52I GLY* 1.3 68.7 + - - +
55I ALA* 4.7 4.3 - - + -
60I HIS* 3.7 39.5 - - + +
83I LEU* 3.9 11.6 - - + +
84I GLN* 3.6 19.1 - - - +
85I ALA* 3.4 36.8 - - + +
89I PRO* 2.8 26.2 + - + +
112I PRO 3.9 3.1 - - - +
113I VAL* 3.7 18.6 - - + -
114I PHE* 4.5 0.7 - - - -
59J MET* 3.7 6.1 - - + +
61J ARG* 4.4 0.3 - - - -
82J SER* 2.8 24.6 + - - -
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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