Contacts of the strand formed by residues 34 - 39 (chain D) in PDB entry 3EYF
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
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Residue Dist Surf HB Arom Phob DC
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4D LEU* 5.1 6.1 - - + -
22D CYS* 4.4 5.6 - - - -
27D PHE* 5.2 1.1 - - + -
29D PHE* 4.0 31.4 - - + +
32D HIS* 4.0 7.6 - - + +
33D GLY* 1.3 81.5 - - - +
35D HIS* 1.3 70.8 + - - +
50D VAL* 3.4 6.3 - - - +
51D ILE* 3.0 37.1 + - + +
70D ILE* 3.9 4.7 - - - +
72D ARG* 3.7 20.4 - - - +
79D MET* 4.3 17.3 - - + -
96D CYS* 4.3 15.3 - - + -
97D ALA 3.7 10.3 - - - +
98D ARG* 4.8 12.3 - - + -
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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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94C TRP* 4.1 17.0 - + - -
97C VAL* 4.9 2.2 - - + -
34D ILE* 1.3 76.7 - - - +
36D TRP* 1.3 65.3 + - - +
47D TRP* 2.9 30.1 + + + +
49D THR 3.2 7.2 - - - +
50D VAL* 3.4 20.8 - - + +
96D CYS* 3.2 9.5 - - - +
97D ALA* 2.9 38.2 + - + +
99D ASP* 2.7 44.4 + - + +
110D GLY* 4.5 3.6 - - - -
112D LEU* 3.5 37.9 - - + +
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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 GLU* 3.8 17.9 - - + -
20D LEU* 3.9 24.9 - - + -
21D SER 3.7 26.5 - - - -
22D CYS* 4.0 2.0 - - + -
35D HIS* 1.3 73.6 - - - +
37D VAL* 1.3 64.2 + - - +
47D TRP* 3.9 1.7 - - - -
48D LEU* 3.0 38.8 + - + +
49D THR* 2.9 18.2 + - + +
70D ILE* 3.8 20.2 - - + -
79D MET* 2.9 38.8 - - + +
81D LEU* 3.6 29.2 - - + +
94D TYR* 3.8 38.6 - + + -
95D TYR 3.2 25.8 - - - -
96D CYS* 3.9 5.4 - - + -
119D THR* 5.1 0.2 - - + -
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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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99C PHE* 4.2 7.9 - - + -
35D HIS* 5.0 0.4 - - + -
36D TRP* 1.3 79.8 - - - +
38D ARG* 1.3 66.1 + - - +
45D LEU* 3.8 32.1 - - + -
46D GLN 3.2 16.8 - - - +
47D TRP* 4.0 16.2 - - + -
48D LEU* 4.1 1.8 - - - -
94D TYR* 3.7 1.2 - - - +
95D TYR* 2.9 34.6 + - + +
97D ALA* 5.4 1.6 - - + -
112D LEU* 3.7 29.4 - - + -
115D TRP* 4.1 18.2 - - + -
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Residues in contact with ARG 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 77.8 - - - +
39D GLN* 1.3 64.2 + - - +
40D ALA* 4.2 5.4 + - + +
44D GLY 3.5 0.5 - - - +
45D LEU* 3.5 7.2 - - - -
46D GLN* 2.6 67.7 + - + +
48D LEU* 3.4 36.2 - - + +
63D SER* 4.5 9.5 + - - -
64D VAL* 4.3 8.5 - - - +
68D PHE* 4.3 2.0 - - - -
89D GLU* 3.3 32.4 + - - +
90D ASP* 3.1 29.2 + - - -
91D MET 5.1 4.2 + - - -
93D LEU 3.3 8.7 - - - +
94D TYR* 3.1 36.6 + - + -
95D TYR* 4.7 0.2 - - - -
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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 HIS* 3.9 15.7 + - - -
87C TYR* 3.5 18.0 + - - -
38D ARG* 1.3 74.9 - - - +
40D ALA* 1.3 66.3 + - - +
41D PRO* 3.8 1.4 - - + +
42D GLY 5.9 0.2 - - - +
43D GLU 3.0 23.4 + - - +
44D GLY 3.4 14.5 + - - +
45D LEU* 3.8 14.8 - - + +
92D GLY* 3.4 1.8 - - - -
93D LEU* 2.7 42.2 + - + +
95D TYR* 2.9 33.4 + - + -
120D MET* 5.6 0.2 - - - +
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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