Contacts of the strand formed by residues 5 - 13 (chain D) in PDB entry 3U53
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 ALA 5 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D ARG* 1.3 75.5 - - - +
6D CYS* 1.3 64.7 + - - +
42D LYS* 4.5 5.6 - - + -
43D GLY* 3.0 26.9 - - - +
44D HIS* 4.1 2.9 - - + +
45D VAL* 4.3 0.7 - - - -
90D THR 2.8 12.2 + - - +
91D VAL* 3.1 17.2 - - + -
92D ILE* 2.8 26.2 + - - +
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Residues in contact with CYS 6 (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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4D ARG* 4.8 0.9 - - - -
5D ALA* 1.3 80.0 - - - +
7D GLY* 1.3 58.7 + - - +
42D LYS* 3.2 3.0 - - - -
43D GLY 2.7 32.4 + - - +
45D VAL* 3.6 17.3 - - - -
51D ASP* 3.3 49.8 - - - +
54D THR* 3.9 5.6 - - - +
55D ALA* 3.8 17.0 - - + +
58D GLU* 4.4 1.6 - - - +
92D ILE* 3.3 20.2 - - - +
94D TRP* 4.3 1.3 - - + -
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Residues in contact with GLY 7 (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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6D CYS* 1.3 75.4 - - - +
8D LEU* 1.3 65.0 + - - +
41D PRO 2.9 18.4 - - - -
42D LYS* 3.6 6.6 - - - +
55D ALA* 3.4 16.7 - - - +
92D ILE 2.9 7.8 + - - +
93D TYR* 3.4 12.1 - - - -
94D TRP* 3.4 17.5 + - - -
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Residues in contact with LEU 8 (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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7D GLY* 1.3 82.7 - - - +
9D ILE* 1.3 61.6 + - - +
10D ILE* 3.0 22.5 + - + +
40D PRO* 3.5 12.0 - - - +
41D PRO* 3.2 8.6 + - - +
52D LEU* 4.2 1.6 - - + -
55D ALA* 3.6 19.1 - - + +
56D LEU* 3.7 28.3 - - + +
59D THR* 3.6 21.9 + - - +
70D LEU* 3.8 15.7 - - + -
72D ILE* 3.6 22.4 - - + -
93D TYR* 3.7 2.2 - - - -
94D TRP* 3.4 21.5 - - + +
96D ALA* 3.9 13.7 - - + -
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Residues in contact with ILE 9 (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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8D LEU* 1.3 68.9 - - - +
10D ILE* 1.3 60.1 + - - +
11D PHE 3.7 0.7 + - - -
26D PHE* 3.5 36.6 - - + -
40D PRO* 4.1 15.5 - - + -
76D PHE* 4.3 20.6 - - + -
93D TYR* 4.0 30.5 - - + -
94D TRP 2.6 13.5 + - - +
95D LEU* 3.5 14.7 - - + +
96D ALA 3.1 20.0 + - - -
131D MET* 5.9 0.7 - - - -
134D ALA* 4.3 23.8 - - + +
135D LEU* 3.9 17.9 - - + -
138D GLY* 5.7 0.9 - - - -
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Residues in contact with ILE 10 (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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8D LEU* 3.0 24.4 + - + +
9D ILE* 1.3 73.3 - - - +
11D PHE* 1.3 64.2 + - - +
26D PHE* 3.4 8.8 - - - +
27D LEU* 3.1 40.0 + - + +
40D PRO* 4.8 2.2 - - - +
41D PRO* 3.8 18.4 - - + -
59D THR* 3.9 24.5 - - + -
65D ILE* 4.7 5.2 - - + -
70D LEU* 4.1 15.0 - - + -
96D ALA* 3.4 9.9 - - + +
98D VAL* 4.0 16.8 - - + -
116D TRP* 3.9 21.1 - - + -
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Residues in contact with PHE 11 (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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9D ILE 4.1 0.7 - - - +
10D ILE* 1.3 76.9 - - - +
12D ARG* 1.3 72.6 + - - +
13D ARG* 4.2 11.9 - - + -
24D ILE* 4.2 5.6 - - + -
25D GLU 3.2 11.0 - - - +
26D PHE* 3.8 17.9 - - + -
73D ILE* 3.7 18.4 - - + -
95D LEU* 4.0 13.2 - - + -
96D ALA 3.1 17.6 + - - -
97D GLU* 3.2 53.8 - - + -
98D VAL* 3.2 26.5 + - - +
116D TRP* 3.8 5.2 - - - -
142D LEU* 3.5 43.3 - - + -
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Residues in contact with ARG 12 (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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11D PHE* 1.3 81.8 - - - +
13D ARG* 1.3 60.1 + - - +
14D CYS* 4.0 0.4 + - - -
24D ILE* 3.5 6.2 - - - +
25D GLU* 2.7 64.6 + - + +
97D GLU* 4.9 1.8 - - - -
98D VAL* 3.6 17.5 - - + -
101D TYR* 3.1 68.7 + - + -
102D ASP* 4.9 1.8 - - - +
116D TRP* 3.3 54.9 - - + +
156D SO4 4.5 10.7 + - - -
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Residues in contact with ARG 13 (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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11D PHE* 4.2 7.4 - - + -
12D ARG* 1.3 74.4 - - - +
14D CYS* 1.3 62.1 + - - +
15D LEU* 3.6 29.7 + - + +
23D ALA* 3.4 7.0 - - + +
24D ILE* 3.9 28.3 - - + +
97D GLU* 3.5 26.4 + - - +
101D TYR* 3.5 14.1 - - - -
142D LEU* 3.5 42.8 + - - +
143D CYS* 5.7 0.6 - - - +
145D ILE* 4.8 6.3 - - - +
146D GLU* 3.8 23.5 - - - +
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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