Contacts of the strand formed by residues 43 - 51 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A PHE* 4.6 5.1 - - - -
42A CYS* 1.3 94.7 + - + +
44A LEU* 1.3 59.8 + - - +
45A LEU* 3.6 21.4 + - + -
97A GLN* 3.9 25.3 + - + +
98A LEU 2.8 28.0 - - - +
99A SER* 3.1 19.7 + - - -
100A PRO* 4.1 1.9 - - - +
118A GLN 3.6 0.9 - - - +
119A GLU* 3.6 2.4 - - - -
120A ARG* 2.9 46.4 + - + +
16B THR* 4.5 13.3 + - - +
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Residues in contact with LEU 44 (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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19A TRP* 3.8 45.8 - - + -
32A PHE* 3.9 37.4 - - + -
43A ARG* 1.3 70.9 - - - +
45A LEU* 1.3 64.2 + - - +
46A LEU* 3.5 28.7 + - + +
96A VAL 3.8 0.2 - - - +
97A GLN* 3.5 1.4 - - - -
98A LEU* 2.8 55.2 + - + +
102A VAL* 4.4 6.1 - - + -
104A PHE* 4.3 7.2 - - + -
118A GLN 3.7 14.8 - - - +
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Residues in contact with LEU 45 (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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16A THR 6.3 0.2 - - - +
43A ARG* 3.8 15.7 - - + -
44A LEU* 1.3 75.8 - - - +
46A LEU* 1.3 60.2 + - - +
47A HIS* 3.7 15.5 + - - +
95A GLY 6.3 0.7 - - - +
96A VAL 3.5 7.2 - - - +
97A GLN* 3.7 35.9 - - + +
117A GLY* 2.9 6.8 - - - -
118A GLN* 2.7 63.4 + - + +
120A ARG* 4.2 28.3 - - + -
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Residues in contact with LEU 46 (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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19A TRP* 4.4 9.6 - - + -
44A LEU* 3.5 12.9 + - + -
45A LEU* 1.3 70.7 - - - +
47A HIS* 1.3 62.7 + - - +
48A THR 4.5 7.6 - - - +
49A ILE* 4.5 2.5 - - + -
64A ILE* 5.2 0.4 - - + -
80A ILE* 3.8 29.6 - - + -
93A MET* 3.2 42.5 - - + +
94A VAL* 4.2 0.9 - - - -
96A VAL* 3.1 26.4 + - + +
98A LEU* 4.0 11.4 - - + -
104A PHE* 4.0 9.9 - - + -
115A LEU* 4.0 23.1 - - + -
116A SER 3.6 14.8 - - - +
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Residues in contact with HIS 47 (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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18A LEU* 5.7 2.4 - - - +
45A LEU* 3.9 17.7 - - + +
46A LEU* 1.3 78.5 - - - +
48A THR* 1.3 67.7 + - + +
92A SER* 3.5 0.9 - - - -
93A MET* 2.9 29.1 + - - -
94A VAL* 3.6 21.3 + - + +
95A GLY 4.9 2.2 - - - -
116A SER* 2.8 22.7 + - - +
117A GLY* 3.7 11.0 - - - -
118A GLN* 2.9 42.6 + - + +
95E GLY 5.1 1.4 + - - -
96E VAL* 3.7 43.7 - - + +
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Residues in contact with THR 48 (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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46A LEU* 4.5 1.3 - - - +
47A HIS* 1.3 86.7 - - + +
49A ILE* 1.3 69.0 + - - +
50A CYS* 3.8 4.5 - - - -
90A MET* 3.8 10.8 - - + -
91A VAL 3.2 9.0 - - - -
92A SER* 3.9 9.9 - - - +
93A MET* 4.8 1.3 - - - +
115A LEU* 3.6 0.3 - - - +
116A SER* 2.7 45.9 + - - +
79E THR 4.0 0.3 + - - -
80E ILE* 2.9 33.0 + - + +
93E MET* 3.7 27.8 - - + -
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Residues in contact with ILE 49 (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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46A LEU* 4.5 4.3 - - + -
48A THR* 1.3 79.6 - - - +
50A CYS* 1.3 64.0 + - - +
62A VAL* 4.4 8.3 - - + -
80A ILE* 3.7 25.6 - - + -
81A ALA* 3.8 13.7 - - + -
83A LEU* 3.4 13.4 - - + +
90A MET* 3.2 4.2 - - - +
91A VAL* 2.9 41.0 + - + -
93A MET* 3.5 29.1 - - + +
113A VAL* 3.5 26.2 - - + -
114A PHE 3.3 6.3 - - - +
115A LEU* 4.0 21.3 - - + -
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Residues in contact with CYS 50 (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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48A THR* 3.8 8.3 - - - -
49A ILE* 1.3 79.9 - - - +
51A LEU* 1.3 62.4 + - - +
83A LEU* 4.3 3.1 - - - -
89A PRO 3.5 4.9 - - - -
90A MET* 3.8 7.4 - - - -
113A VAL* 3.4 2.5 - - - -
114A PHE* 2.7 39.9 + - + -
79E THR* 3.9 16.6 - - + -
80E ILE 3.8 8.5 - - - -
81E ALA* 3.6 34.8 - - - -
82E SER* 3.3 21.5 - - - +
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Residues in contact with LEU 51 (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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50A CYS* 1.3 72.7 - - - +
52A GLY* 1.3 64.5 + - - +
55A ALA* 4.4 5.4 - - + -
60A HIS* 3.7 37.7 - - + +
83A LEU* 3.9 13.9 - - + +
84A GLN* 3.6 16.8 - - - +
85A ALA* 3.5 38.8 - - + +
89A PRO* 2.8 25.8 + - + +
112A PRO 3.8 4.0 - - - +
113A VAL* 3.9 16.2 - - + -
114A PHE* 4.5 0.9 - - - -
59E MET* 2.8 11.3 - - - +
82E SER* 2.8 22.5 + - - -
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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