Contacts of the strand formed by residues 57 - 65 (chain D) in PDB entry 1MDU
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 LEU 57 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLY 3.7 23.6 - - - +
13D LYS 3.7 16.6 - - - +
14D GLU 4.5 0.2 - - - +
15D PRO* 4.0 27.6 - - + -
49D THR* 4.1 12.3 - - + -
50D VAL 3.4 8.3 - - - +
51D GLN* 4.3 5.8 - - + -
52D LEU* 5.0 2.8 - - - +
55D GLY 4.5 7.9 - - - +
56D ASN* 1.3 82.9 - - - +
58D GLN* 1.3 59.5 + - - +
59D TYR* 3.7 20.9 - - + +
91D ARG* 4.0 19.2 + - - +
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Residues in contact with GLN 58 (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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48D LYS 3.6 1.0 - - - +
49D THR* 3.4 5.9 - - - -
50D VAL* 2.8 52.3 + - + +
52D LEU* 3.5 37.2 - - + +
57D LEU* 1.3 73.6 - - - +
59D TYR* 1.3 65.6 + - - +
60D ASP* 3.6 18.4 - - - +
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Residues in contact with TYR 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D GLY* 2.7 32.6 + - - -
47D LEU* 4.0 13.2 - - + -
48D LYS 3.5 1.3 - - - -
49D THR* 3.3 35.2 - - + -
57D LEU* 3.7 21.5 - - + +
58D GLN* 1.3 81.3 - - - +
60D ASP* 1.3 69.1 + - - +
61D LEU 4.1 0.4 - - - -
88D LEU* 3.8 31.9 - - + +
91D ARG* 4.0 44.8 + - + +
92D ALA* 3.5 19.0 - - + -
93D VAL* 3.2 21.1 + - - +
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Residues in contact with ASP 60 (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 ILE 3.6 0.7 - - - +
47D LEU* 3.7 1.1 - - - -
48D LYS* 3.0 35.7 + - + +
50D VAL* 5.8 1.2 - - - +
58D GLN* 3.6 22.2 - - - +
59D TYR* 1.3 80.5 - - - +
61D LEU* 1.3 61.6 + - - +
62D HIS* 3.6 13.1 - - - +
93D VAL* 3.6 14.4 - - - +
95D HIS* 3.0 24.1 + - - +
105D THR* 6.0 2.2 - - - -
109D TYR* 3.6 22.2 - - - +
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Residues in contact with LEU 61 (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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45D VAL* 4.1 11.2 - - + -
46D ILE 3.4 11.9 - - - +
47D LEU* 3.8 23.8 - - + -
59D TYR 4.1 0.6 - - - -
60D ASP* 1.3 72.4 - - - +
62D HIS* 1.3 54.7 + - - +
81D THR* 3.5 38.6 - - + +
84D LEU* 3.6 30.5 - - + -
85D ASP* 3.7 18.4 - - + +
88D LEU* 5.0 1.3 - - + -
92D ALA* 3.8 19.3 - - + +
93D VAL 2.9 12.9 + - - +
94D GLN* 3.3 4.1 - - + -
95D HIS* 2.7 34.0 + - - +
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Residues in contact with HIS 62 (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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44D TYR 3.8 0.3 - - - +
45D VAL* 3.4 2.8 - - - +
46D ILE* 2.6 48.1 + - + +
60D ASP* 3.6 14.5 - - - +
61D LEU* 1.3 79.3 - - - +
63D TYR* 1.3 60.9 + - - +
64D TRP 4.0 0.2 - - - -
81D THR* 4.9 2.0 - - - -
95D HIS* 3.1 36.9 - + - +
97D GLU* 2.9 31.1 + - + +
103D SER* 4.5 4.0 - - - -
105D THR* 4.6 4.9 - - + -
106D PHE* 3.8 30.4 - + + -
109D TYR* 3.0 40.0 + + - -
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Residues in contact with TYR 63 (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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44D TYR 3.2 8.7 - - - +
45D VAL* 4.4 1.1 - - + +
62D HIS* 1.3 73.6 - - - +
64D TRP* 1.3 54.5 + - - +
65D LEU* 4.5 11.5 - - + +
77D ALA* 3.9 12.3 - - + +
78D ALA* 4.1 16.6 - - + -
81D THR* 3.4 31.9 - - + +
94D GLN* 4.9 0.9 - - + -
95D HIS 2.9 29.5 + - - -
96D ARG* 3.5 27.8 - - + +
97D GLU* 2.8 30.6 + - - +
148E GLY 3.2 27.1 - - - -
149E ARG* 3.5 4.0 - - - +
150E THR* 3.0 44.4 + - + -
151E THR* 4.4 1.4 + - - -
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Residues in contact with TRP 64 (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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38D PHE* 3.5 26.9 - + + -
39D PHE 3.5 17.7 - - - -
40D THR* 4.3 2.5 - - - -
42D ASP 3.9 2.2 - - - -
43D ALA* 3.4 2.9 - - - -
44D TYR* 2.8 49.8 + + + +
46D ILE* 4.1 19.3 - - + -
62D HIS 4.0 1.2 + - - -
63D TYR* 1.3 72.5 - - - +
65D LEU* 1.3 63.3 + - - +
66D GLY* 3.4 28.0 - - - -
97D GLU* 3.2 16.6 - - + -
99D GLN* 3.6 36.2 - - + +
102D GLU* 2.7 39.2 + - + +
106D PHE* 3.8 16.9 - + + -
114D LEU* 4.8 1.0 - - - +
116D TYR* 3.6 18.1 - + - -
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Residues in contact with LEU 65 (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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42D ASP 4.4 1.3 - - - -
43D ALA* 4.1 7.6 - - + +
63D TYR* 4.5 9.6 - - + +
64D TRP* 1.3 83.7 - - - +
66D GLY* 1.3 64.1 + - - +
67D ASN* 5.1 0.3 + - - -
69D CYS* 4.2 9.0 - - - -
74D SER* 3.5 37.0 - - - +
77D ALA* 4.3 9.2 - - + -
96D ARG* 3.6 45.3 - - + +
97D GLU 2.9 13.0 + - - +
98D VAL* 4.1 8.4 - - + +
99D GLN* 3.1 24.4 + - - +
148E GLY* 3.8 8.7 - - - +
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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