Contacts of the strand formed by residues 87 - 98 (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 LYS 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B PRO* 5.3 11.0 - - + -
83D VAL* 4.1 2.9 - - - +
84D ALA 2.6 40.8 + - - +
85D ARG 4.3 2.7 - - - +
86D ASN* 1.3 78.7 - - - +
88D PRO* 1.3 67.2 - - + +
89D LYS* 3.5 25.0 - - - +
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Residues in contact with PRO 88 (chain D).
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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83B VAL* 4.3 29.8 - - + -
86B ASN* 4.7 13.5 - - - +
88B PRO* 4.8 15.7 - - + -
4D ARG 6.0 0.2 + - - -
82D TYR 3.4 7.6 - - - +
83D VAL* 4.0 18.8 - - + -
86D ASN 4.5 3.1 - - - +
87D LYS* 1.3 84.6 - - + +
89D LYS* 1.3 67.0 + - - +
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Residues in contact with LYS 89 (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 5.6 2.0 - - - +
80D LEU 4.3 0.7 - - - -
81D ASN* 3.6 4.5 - - - +
82D TYR* 2.7 68.7 + - + +
84D ALA* 3.8 18.6 + - + +
87D LYS* 3.5 34.1 - - - +
88D PRO* 1.3 80.8 - - - +
90D THR* 1.3 68.8 + - - +
91D VAL* 4.8 2.5 - - + -
160D SO4 4.6 9.6 - - - +
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Residues in contact with THR 90 (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* 3.4 32.0 - - - +
5D ALA* 2.8 25.3 + - - +
79D GLU* 4.1 10.8 - - + +
80D LEU 3.2 6.5 - - - +
81D ASN* 2.8 22.4 + - - +
89D LYS* 1.3 74.6 + - - +
91D VAL* 1.3 68.4 + - - +
92D ILE* 3.9 22.7 - - + -
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Residues in contact with VAL 91 (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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5D ALA* 3.1 20.4 - - + +
42D LYS* 3.9 17.0 - - + -
78D ARG 3.9 0.9 - - - +
79D GLU* 3.4 2.3 - - - -
80D LEU* 2.7 42.2 + - + +
82D TYR* 3.7 31.9 - - + +
89D LYS* 4.8 2.7 - - + -
90D THR* 1.3 81.1 - - - +
92D ILE* 1.3 70.0 + - - +
93D TYR* 3.5 38.8 + - + +
131D MET* 6.2 0.4 - - + -
160D SO4 5.2 0.2 - - - +
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Residues in contact with ILE 92 (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* 4.2 17.7 - - - +
5D ALA 2.8 13.9 + - - +
6D CYS* 3.3 14.9 - - - +
7D GLY 2.9 25.3 + - - +
51D ASP* 4.6 5.8 - - - +
77D LYS* 4.1 24.7 - - + -
78D ARG 3.6 10.5 - - - +
79D GLU* 3.4 38.8 - - + +
90D THR* 3.9 11.4 - - + -
91D VAL* 1.3 76.9 - - - +
93D TYR* 1.3 64.8 + - - +
94D TRP* 4.0 24.6 - - + -
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Residues in contact with TYR 93 (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* 3.4 32.8 - - - -
8D LEU 3.7 8.1 - - - -
9D ILE* 4.0 24.7 - - + -
40D PRO* 3.9 24.6 - - + +
42D LYS* 3.0 29.5 + - + +
76D PHE* 4.6 1.4 - - - -
77D LYS* 3.5 6.6 - - - +
78D ARG* 2.9 36.3 + - + +
80D LEU* 3.9 23.1 - - + -
91D VAL* 3.5 19.4 - - + +
92D ILE* 1.3 73.9 - - - +
94D TRP* 1.3 65.1 + - - +
131D MET* 3.2 37.9 - - + +
134D ALA* 5.2 2.0 - - + -
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Residues in contact with TRP 94 (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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140A GLN* 5.0 5.5 - - - +
6D CYS* 4.3 1.3 - - + -
7D GLY 3.4 15.0 + - - -
8D LEU* 3.4 16.3 - - + -
9D ILE* 2.6 33.4 + - - +
51D ASP* 3.6 43.3 - - + -
52D LEU* 3.3 40.2 - - + +
55D ALA* 4.1 4.3 - - + -
72D ILE* 4.6 11.4 - - + -
73D ILE 5.4 1.1 - - - -
76D PHE* 3.4 28.5 - - - -
77D LYS* 3.5 35.6 - - + +
92D ILE* 4.0 25.4 - - + -
93D TYR* 1.3 78.1 - - - +
95D LEU* 1.3 60.3 + - - +
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Residues in contact with LEU 95 (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* 3.5 31.4 - - + +
11D PHE* 4.0 13.9 - - + -
26D PHE* 4.6 2.9 - - + -
72D ILE* 3.6 6.6 - - - +
73D ILE* 2.8 39.2 + - + +
76D PHE* 3.6 28.6 + - + -
94D TRP* 1.3 76.3 - - - +
96D ALA* 1.3 60.9 + - - +
138D GLY* 4.0 21.8 - - - +
141D PHE* 3.7 32.1 - - + -
142D LEU* 4.1 15.9 - - + -
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Residues in contact with ALA 96 (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* 3.9 32.8 - - + -
9D ILE 3.1 7.5 + - - -
10D ILE* 3.4 12.8 - - + +
11D PHE* 3.1 27.1 + - - -
70D LEU* 4.4 9.6 - - + -
71D THR 3.0 16.8 - - - +
72D ILE* 4.2 4.5 - - + -
94D TRP 4.0 0.4 + - - -
95D LEU* 1.3 75.0 - - - +
97D GLU* 1.3 60.3 + - - +
98D VAL 4.0 0.2 + - - -
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Residues in contact with GLU 97 (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* 3.2 39.7 - - + +
12D ARG* 4.9 2.2 - - - -
13D ARG* 3.5 38.4 + - - +
70D LEU* 3.4 4.2 - - - -
71D THR* 2.8 42.7 + - - +
73D ILE* 4.2 13.1 - - + +
96D ALA* 1.3 73.2 - - - +
98D VAL* 1.3 76.7 + - - +
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Residues in contact with VAL 98 (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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10D ILE* 4.0 24.2 - - + -
11D PHE 3.2 3.1 + - - +
12D ARG* 3.6 31.4 - - + -
65D ILE* 4.6 3.8 - - + -
69D GLN 3.7 5.4 - - - +
70D LEU* 4.0 14.4 - - + -
71D THR* 5.9 0.2 - - - -
97D GLU* 1.3 86.6 - - - +
99D LYS* 1.3 65.5 + - - +
100D ASP* 3.4 25.2 - - - +
101D TYR* 4.3 2.0 + - - -
103D VAL* 3.9 21.3 - - + -
116D TRP* 4.3 6.3 - - + -
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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