Contacts of the strand formed by residues 43 - 51 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D PHE* 4.8 1.1 - - - -
42D CYS* 1.3 87.1 + - - +
44D LEU* 1.3 62.1 + - - +
45D LEU* 3.8 12.3 + - + -
97D GLN* 3.7 38.2 + - + +
98D LEU 3.1 9.2 - - - +
99D SER* 2.5 39.8 + - - +
100D PRO* 4.5 1.1 - - - -
118D GLN 3.7 0.7 - - - +
119D GLU* 3.8 1.9 - - - -
120D ARG* 3.0 37.7 + - + +
121D TYR* 6.4 1.1 - - + -
118E GLN* 5.1 2.8 - - - +
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D TRP* 3.6 48.5 - - + -
32D PHE* 3.9 26.6 - - + -
43D ARG* 1.3 72.6 - - - +
45D LEU* 1.3 65.0 + - - +
46D LEU* 3.5 4.6 + - + +
96D VAL 3.8 0.2 - - - +
97D GLN* 3.4 2.3 - - - -
98D LEU* 2.7 50.1 + - + +
102D VAL* 3.9 12.8 - - + -
104D PHE* 3.9 35.2 - - + -
118D GLN 3.7 15.5 - - - +
119D GLU* 4.4 2.5 - - + +
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Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D THR* 6.4 0.2 - - + -
43D ARG* 4.1 7.2 - - + +
44D LEU* 1.3 74.9 - - - +
46D LEU* 1.2 63.7 + - - +
47D HIS* 3.6 15.2 + - + +
96D VAL 3.6 5.4 - - - +
97D GLN* 4.1 34.1 - - + +
117D GLY* 2.8 6.4 - - - -
118D GLN* 2.8 62.8 + - + +
120D ARG* 3.9 34.5 - - + -
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D TRP* 4.3 8.1 - - + -
44D LEU* 3.5 6.8 + - + +
45D LEU* 1.2 75.0 - - - +
47D HIS* 1.3 61.8 + - - +
48D THR 5.1 0.7 - - - +
49D ILE* 5.0 2.0 - - + -
64D ILE* 5.5 0.9 - - + -
80D ILE* 4.2 17.7 - - + -
93D MET* 2.8 57.8 - - + +
94D VAL* 4.1 0.7 - - - -
95D GLY 4.4 0.2 + - - -
96D VAL* 3.1 35.5 + - + +
98D LEU* 4.6 12.1 - - + -
104D PHE* 4.3 20.0 - - + -
115D LEU* 4.3 17.7 - - + -
116D SER 3.9 12.1 - - - +
117D GLY* 4.2 0.4 - - - -
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Residues in contact with HIS 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ILE* 6.3 1.7 - - + +
93C MET* 6.0 0.2 - - - -
95C GLY 5.3 0.8 + - - -
96C VAL* 3.7 45.0 - - + +
98C LEU* 5.5 1.1 - - + +
18D LEU* 5.4 2.8 - - - +
45D LEU* 3.6 17.8 + - + +
46D LEU* 1.3 78.2 - - - +
48D THR* 1.3 64.6 + - + +
92D SER* 3.5 0.7 + - - -
93D MET* 2.6 38.7 + - - +
94D VAL* 3.7 14.0 + - + +
95D GLY 5.4 1.1 - - - -
116D SER* 2.8 21.3 + - - +
117D GLY* 3.7 11.4 + - - -
118D GLN* 3.0 44.7 + - + +
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Residues in contact with THR 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C THR 3.9 1.0 + - - +
80C ILE* 3.0 32.1 + - + +
93C MET* 3.8 26.9 - - + -
46D LEU* 5.1 0.9 - - - +
47D HIS* 1.3 89.0 - - + +
49D ILE* 1.3 65.8 - - - +
50D CYS* 3.7 4.1 - - - -
90D MET* 3.8 10.8 - - + -
91D VAL 3.3 8.3 - - - -
92D SER* 4.1 10.8 - - - +
93D MET* 4.5 0.7 - - - -
114D PHE 4.1 0.2 - - - +
115D LEU* 3.5 4.0 - - - +
116D SER* 2.8 46.5 + - - +
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Residues in contact with ILE 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 4.9 1.3 - - + -
48D THR* 1.3 78.2 - - - +
50D CYS* 1.3 63.4 + - - +
62D VAL* 4.4 10.3 - - + -
80D ILE* 3.9 19.3 - - + -
81D ALA* 3.7 14.4 - - + -
83D LEU* 3.6 12.4 - - + +
90D MET* 3.1 4.9 - - - +
91D VAL* 2.9 39.9 + - + -
93D MET* 3.2 37.7 - - + -
113D VAL* 3.5 25.1 - - + -
114D PHE 3.3 7.0 - - - +
115D LEU* 4.0 19.5 - - + -
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Residues in contact with CYS 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C THR* 3.9 16.8 - - + -
80C ILE 3.7 11.0 - - - -
81C ALA* 3.6 32.1 - - - -
82C SER* 3.3 18.8 - - - +
48D THR* 3.7 7.4 - - - -
49D ILE* 1.3 79.6 - - - +
51D LEU* 1.3 62.0 + - - +
83D LEU* 4.5 0.9 - - - -
89D PRO 3.6 5.6 - - - -
90D MET* 3.7 12.6 - - - -
113D VAL* 3.6 5.6 - - - -
114D PHE* 2.8 34.4 + - - +
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C MET* 3.7 10.6 - - + +
61C ARG* 4.5 0.2 - - - -
82C SER* 2.8 29.6 + - - -
50D CYS* 1.3 72.1 - - - +
52D GLY* 1.3 67.7 + - - +
55D ALA* 4.5 4.5 - - + -
60D HIS* 3.7 38.1 - - + +
83D LEU* 3.9 11.0 - - + +
84D GLN* 3.5 18.6 - - - +
85D ALA* 3.3 37.5 - - + +
89D PRO* 2.8 21.8 + - + +
112D PRO 3.8 3.1 - - - +
113D VAL* 3.9 20.0 - - + -
114D PHE* 4.5 1.1 - - - -
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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