Contacts of the strand formed by residues 69 - 76 (chain D) in PDB entry 1D1T
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 69 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D ILE* 4.2 12.6 - - + -
42D ALA 3.1 13.9 - - - +
43D THR* 3.7 2.7 - - - -
67D HIS 3.9 2.4 + - - -
68D GLU* 1.3 76.0 - - - +
70D THR* 1.3 63.2 + - - +
90D ILE* 3.5 22.3 - - - +
91D PRO* 3.5 14.8 + - + +
145D THR* 3.5 30.5 - - + +
170D CYS* 3.7 11.2 + - - -
173D GLY* 4.8 1.8 - - - -
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Residues in contact with THR 70 (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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40D ILE* 4.0 2.4 - - - +
41D LEU* 2.9 22.8 + - + +
42D ALA 2.9 11.7 + - - +
69D ALA* 1.3 74.0 + - - +
71D GLY* 1.3 61.8 + - - +
88D LYS* 4.2 10.8 - - + -
89D VAL 3.5 10.5 - - - +
90D ILE* 4.3 1.3 - - - +
91D PRO* 4.9 0.9 - - - -
160D ILE* 4.0 12.6 - - + -
166D PRO* 3.0 39.0 + - + -
169D VAL* 3.6 13.9 + - + +
170D CYS* 3.0 28.3 + - - -
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Residues in contact with GLY 71 (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 ILE* 3.7 11.4 - - - +
39D LYS 3.2 14.4 - - - -
40D ILE* 4.4 1.3 - - - -
41D LEU* 4.0 4.9 - - - +
69D ALA 4.4 0.2 - - - -
70D THR* 1.3 75.0 - - - +
72D ILE* 1.3 65.6 + - - +
88D LYS* 3.5 9.9 - - - +
89D VAL* 2.8 38.3 + - - -
91D PRO* 4.7 1.8 - - - +
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Residues in contact with ILE 72 (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 ILE* 3.4 3.9 - - - +
39D LYS* 2.8 43.1 + - + +
41D LEU* 3.6 32.1 - - + -
71D GLY* 1.3 76.8 - - - +
73D VAL* 1.3 68.3 + - - +
74D GLU 3.2 0.3 + - - -
86D GLY* 3.6 37.2 - - - +
87D ASP 3.3 6.3 - - - +
88D LYS* 4.2 19.1 - - + -
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Residues in contact with VAL 73 (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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36D VAL* 3.5 27.6 - - + -
37D ARG 3.8 3.1 - - - -
38D ILE* 4.5 2.7 - - - +
72D ILE* 1.3 74.4 - - - +
74D GLU* 1.3 63.1 + - - +
75D SER 3.9 9.0 - - - +
76D ILE* 3.8 20.9 - - + -
83D VAL* 4.1 8.3 - - + -
84D LYS 3.5 15.5 - - - +
85D PRO* 3.4 1.6 - - + +
86D GLY 2.8 26.0 + - - -
87D ASP* 2.9 26.3 + - + +
89D VAL* 3.6 26.0 - - + -
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Residues in contact with GLU 74 (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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2D THR* 2.7 34.9 + - - +
3D ALA* 4.7 2.8 - - - +
7D ILE* 3.4 4.5 - - + +
37D ARG* 2.7 51.2 + - - +
39D LYS* 4.6 2.5 - - + +
72D ILE* 3.2 5.8 + - - +
73D VAL* 1.3 74.1 - - - +
75D SER* 1.3 87.6 + - - +
85D PRO* 3.8 13.2 - - - +
149D TYR* 4.1 28.5 - - + +
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Residues in contact with SER 75 (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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3D ALA* 3.9 24.5 - - - -
4D GLY 4.8 1.3 + - - -
31D PRO* 3.5 19.4 - - - +
36D VAL* 3.9 0.7 - - - -
37D ARG* 2.9 29.7 + - - +
73D VAL* 3.5 3.0 - - - +
74D GLU* 1.3 104.5 + - - +
76D ILE* 1.3 65.1 + - - +
85D PRO* 4.1 10.1 - - - -
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Residues in contact with ILE 76 (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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31D PRO* 4.0 5.7 - - - +
35D GLU 4.0 3.6 - - - -
36D VAL* 4.4 2.2 - - + +
73D VAL* 3.8 13.7 - - + -
75D SER* 1.3 77.4 - - - +
77D GLY* 1.3 65.4 + - - +
80D VAL* 3.7 25.1 - - + +
83D VAL* 3.3 47.6 - - + +
84D LYS* 4.1 4.9 - - + -
85D PRO* 4.2 17.9 - - + +
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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