Contacts of the strand formed by residues 35 - 44 (chain C) 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 GLU 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C PRO* 3.8 5.6 - - + -
32C LYS* 2.9 32.5 + - - +
33C THR 3.4 13.7 - - - +
34C LYS* 1.3 78.7 - - - +
36C VAL* 1.3 69.5 + - - +
77C GLY 2.7 23.9 + - - -
80C VAL* 3.2 1.4 - - - +
123C LEU* 3.7 14.9 - - + +
125C ASP* 4.0 4.5 + - - +
129C ARG* 2.8 46.0 + - - -
151C VAL* 3.4 11.4 - - + +
152C VAL 3.5 11.4 - - - +
153C ASP* 4.4 11.7 - - - +
154C GLU 4.2 0.2 - - - +
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Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLU* 1.3 82.9 - - - +
37C ARG* 1.3 61.2 + - - +
38C ILE* 3.8 16.3 + - + -
73C VAL* 3.7 34.5 - - + -
75C SER 3.9 4.0 - - - +
76C ILE* 4.7 1.8 - - - -
80C VAL* 3.9 13.2 - - + -
83C VAL* 3.7 22.9 - - + -
151C VAL* 3.4 3.6 - - - -
152C VAL* 2.8 38.2 + - - +
154C GLU* 4.5 6.3 - - + -
157C VAL* 3.9 24.2 - - + -
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Residues in contact with ARG 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C THR 3.1 18.6 + - - -
4C GLY 4.3 1.8 - - - +
5C LYS 2.8 26.4 + - - -
7C ILE* 3.4 22.2 - - - +
28C VAL* 2.6 50.5 + - + -
29C ALA 3.3 6.8 + - - -
30C PRO* 3.8 12.6 - - - +
31C PRO* 3.9 8.6 - - + +
36C VAL* 1.3 72.5 - - - +
38C ILE* 1.3 59.8 + - - +
73C VAL* 3.8 3.3 - - - -
74C GLU* 2.8 52.7 + - - +
75C SER* 3.1 22.0 + - - +
149C TYR* 4.3 11.0 - - + -
150C THR 3.2 15.0 - - - +
151C VAL* 3.7 11.0 - - + -
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Residues in contact with ILE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C VAL* 3.9 18.8 - - + +
37C ARG* 1.3 78.1 - - - +
39C LYS* 1.3 76.0 + - - +
40C ILE* 3.7 10.3 + - + -
71C GLY* 3.9 10.3 - - - +
72C ILE 3.5 16.4 - - - +
73C VAL* 4.8 0.9 - - - -
89C VAL* 3.6 24.0 - - + -
91C PRO* 4.7 17.3 - - + -
149C TYR* 3.1 8.3 - - - -
150C THR* 2.7 48.3 + - + +
152C VAL* 3.7 26.2 - - + -
157C VAL* 4.6 5.6 - - + -
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Residues in contact with LYS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ARG 4.4 0.2 + - - -
38C ILE* 1.3 70.8 - - - +
40C ILE* 1.3 68.2 + - - +
41C LEU* 3.5 13.4 + - + +
71C GLY* 3.1 4.5 - - - -
72C ILE* 2.9 44.7 + - + +
74C GLU* 4.6 4.0 - - + +
148C GLU* 3.4 11.4 - - + +
149C TYR* 3.6 39.3 + - + +
374C PHE 6.1 0.4 - - - -
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Residues in contact with ILE 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE* 4.0 16.2 - - + +
39C LYS* 1.3 77.6 - - - +
41C LEU* 1.3 62.4 + - - +
42C ALA 3.8 17.7 - - - +
69C ALA* 4.1 10.5 - - + -
70C THR 4.0 3.1 - - - +
71C GLY* 5.1 0.2 - - - -
91C PRO* 5.0 4.9 - - + -
145C THR* 3.6 36.6 - - + +
147C THR* 3.1 25.6 - - + +
148C GLU 3.0 9.5 + - - +
149C TYR 4.7 0.2 - - - +
150C THR* 3.9 24.7 - - + -
374C PHE* 3.3 37.7 - - + +
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LYS* 3.5 13.4 + - + +
40C ILE* 1.3 75.8 - - - +
42C ALA* 1.3 64.5 + - - +
70C THR 2.9 12.2 + - - +
71C GLY* 4.2 9.0 - - - +
72C ILE* 3.6 37.9 - - + -
88C LYS* 4.6 4.0 - - + -
166C PRO* 3.7 33.9 - - + +
373C THR* 3.9 4.7 + - - -
374C PHE* 3.2 29.1 + - - +
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Residues in contact with ALA 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ILE* 3.7 2.5 - - - +
41C LEU* 1.3 81.6 - - - +
43C THR* 1.3 60.9 + - - +
69C ALA* 3.0 20.9 - - - +
70C THR 3.0 11.0 + - - -
166C PRO* 3.7 19.5 - - + +
167C GLU* 3.8 11.0 - - + +
170C CYS* 3.9 3.1 - - - +
371C VAL* 3.7 18.6 - - + -
372C LEU 3.1 13.9 - - - +
373C THR* 4.4 4.7 - - - +
374C PHE* 4.4 2.0 - - - -
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Residues in contact with THR 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ILE* 4.2 0.9 - - - -
42C ALA* 1.3 75.1 - - - +
44C GLY* 1.3 58.7 + - - +
68C GLU 2.9 13.9 + - - -
69C ALA* 3.5 9.0 - - - +
145C THR* 2.7 37.0 + - - +
146C PHE* 3.5 30.5 - - + -
170C CYS* 4.8 0.2 - - - -
371C VAL* 4.4 2.7 - - - -
372C LEU* 2.7 49.1 + - + +
374C PHE* 3.9 16.4 - - + -
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Residues in contact with GLY 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C THR* 1.3 77.1 + - - +
45C ILE* 1.3 62.3 + - - -
46C CYS 3.5 5.5 + - - -
49C ASP* 4.2 2.1 - - - +
68C GLU* 2.8 38.6 + - - +
146C PHE* 3.8 12.7 - - - -
170C CYS* 4.2 4.6 - - - -
369C ARG* 5.0 1.1 - - - -
370C THR 3.1 11.2 - - - -
371C VAL* 4.1 8.1 - - - -
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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