Contacts of the strand formed by residues 34 - 40 (chain D) in PDB entry 3DIF
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 ILE 34 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 4.2 15.5 - - + -
22D CYS* 4.5 5.2 - - - +
24D ALA* 5.0 0.9 - - + -
27D TYR* 3.5 24.2 - - - +
29D PHE* 4.4 9.2 - - + +
32D TYR 4.8 1.6 - - - +
33D TYR* 1.3 81.3 - - - +
35D HIS* 1.3 62.6 + - - +
36D TRP* 4.0 14.2 - - - +
49D GLY 4.0 0.2 - - - +
50D TRP* 3.1 3.5 - - - -
51D VAL* 2.9 42.0 + - + +
53D PRO* 4.3 17.3 - - + -
79D ALA* 3.9 26.5 - - + -
96D CYS* 4.1 18.6 - - + -
97D ALA 3.6 5.2 - - - +
98D ARG* 4.3 4.5 - - + -
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Residues in contact with HIS 35 (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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62B GLU* 5.0 1.0 + - - -
91C HIS* 5.4 3.6 - + - -
96C TRP* 4.5 10.3 - + - -
33D TYR* 3.5 31.3 - + + +
34D ILE* 1.3 73.6 - - - +
36D TRP* 1.3 63.9 + - - +
37D VAL* 4.9 0.2 - - - -
47D TRP* 3.2 22.6 + - + +
49D GLY 3.4 2.7 - - - +
50D TRP* 3.4 31.6 - + + +
96D CYS* 3.1 6.9 - - - +
97D ALA* 2.7 47.8 + - + +
98D ARG* 4.8 4.7 - - - -
99D GLY* 4.9 5.5 + - - -
105D TRP* 5.7 7.6 - + + +
106D PHE* 3.7 32.4 - + + -
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Residues in contact with TRP 36 (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 GLN* 4.4 6.7 - - - -
20D ILE* 3.7 30.1 - - + -
21D SER 4.1 11.7 - - - -
22D CYS* 3.6 31.2 - - + -
34D ILE* 4.0 14.8 + - + +
35D HIS* 1.3 77.6 - - - +
37D VAL* 1.3 60.5 + - - +
47D TRP* 3.8 2.4 - - - -
48D ILE* 2.8 37.8 + - + -
49D GLY 2.9 10.7 + - - +
51D VAL* 4.8 2.6 - - - +
70D LEU* 3.7 26.6 - - + +
79D ALA* 4.2 6.2 - - + +
80D TYR 3.9 30.6 + - - -
81D MET* 3.6 37.5 - - + -
95D PHE 3.3 22.2 - - - -
96D CYS* 3.9 13.7 - - + -
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Residues in contact with VAL 37 (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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98C PHE* 4.4 6.1 - - + -
35D HIS 4.9 1.6 - - - -
36D TRP* 1.3 82.2 - - - +
38D LYS* 1.3 62.7 + - - +
45D LEU* 3.9 24.7 - - + -
46D GLU 3.2 25.4 - - - +
47D TRP* 4.5 6.1 - - + -
48D ILE* 4.0 4.2 - - - +
93D VAL 3.9 0.3 - - - +
94D TYR* 3.4 6.4 - - - -
95D PHE* 2.8 37.2 + - + +
97D ALA* 4.9 2.5 - - + -
106D PHE* 4.2 23.3 - - + -
109D TRP* 4.1 29.6 - - + -
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Residues in contact with LYS 38 (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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37D VAL* 1.3 75.0 - - - +
39D GLN* 1.3 63.6 + - - +
40D ARG* 3.9 19.0 - - + +
43D GLN* 5.2 1.8 + - - -
44D GLY 3.5 1.2 - - - +
45D LEU* 3.4 6.2 - - - -
46D GLU* 2.7 61.8 + - + +
48D ILE* 4.0 7.4 - - + +
63D LYS* 5.0 5.7 - - - +
64D PHE* 3.9 25.4 - - + -
67D LYS* 6.0 0.2 - - - +
89D GLU* 2.9 30.1 + - - +
90D ASP* 3.9 9.3 + - - +
92D ALA* 3.8 7.4 - - + -
93D VAL 3.9 2.2 - - - -
94D TYR* 3.3 38.4 + - + +
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Residues in contact with GLN 39 (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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38C GLN* 2.8 37.3 + - - +
87C TYR* 4.2 6.0 + - - -
38D LYS* 1.3 74.3 - - - +
40D ARG* 1.3 67.7 + - - +
41D PRO* 4.6 2.8 - - + +
44D GLY* 2.7 39.3 + - - -
45D LEU* 3.4 16.1 - - + +
92D ALA* 3.3 2.5 - - - +
93D VAL* 2.9 53.1 + - + +
95D PHE* 3.7 18.4 - - + -
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Residues in contact with ARG 40 (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 LYS* 3.9 12.1 - - + +
39D GLN* 1.3 80.4 + - - +
41D PRO* 1.3 75.8 - - + +
42D GLY 3.2 2.6 + - - +
43D GLN* 3.2 44.2 + - + +
44D GLY* 3.2 16.6 + - - +
46D GLU* 4.8 1.5 + - - +
88D SER* 3.2 19.2 + - - -
89D GLU* 3.0 53.6 + - - +
91D SER* 2.9 16.9 + - - +
92D ALA* 3.7 17.7 - - + -
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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
------------------------------------------------------------
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