Contacts of the strand formed by residues 34 - 40 (chain D) in PDB entry 4F9P
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* 5.3 6.7 - - + -
22D CYS* 5.8 2.5 - - + -
24D ALA* 6.0 5.4 - - + -
29D PHE* 5.4 9.6 - - + -
32D TYR* 4.2 7.2 - - + +
33D LEU* 1.3 79.2 - - - +
35D HIS* 1.3 63.3 + - - +
36D TRP* 3.1 36.8 - - + +
50D VAL* 2.5 38.1 - - - +
51D ILE* 3.6 24.2 + - + +
53D PRO* 5.5 2.2 - - + -
79D ALA* 3.7 28.5 - - + -
96D CYS* 5.1 4.0 - - + -
97D ALA 3.1 11.4 - - - +
98D ARG* 3.9 13.0 - - + -
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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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33D LEU* 4.5 6.2 - - + +
34D ILE* 1.3 79.6 + - - +
36D TRP* 1.3 82.4 + - - +
37D ILE* 5.3 2.5 - - + -
47D TRP* 3.1 24.8 + + + +
49D GLY 3.8 0.4 - - - -
50D VAL* 2.9 28.6 - - + +
96D CYS* 3.4 15.1 - - - +
97D ALA* 2.8 30.0 + - + +
99D SER* 3.7 6.7 - - - -
100D ASP* 2.9 39.5 + - + +
232D HIS* 3.8 25.9 + + - -
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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 GLN* 4.7 7.0 - - - -
20D VAL* 3.9 26.2 - - + -
21D SER 4.4 0.9 - - - -
22D CYS* 3.5 26.9 - - + -
34D ILE* 3.1 22.7 - - + +
35D HIS* 1.3 89.7 - - - +
37D ILE* 1.3 61.3 + - - +
47D TRP* 3.4 2.9 - - - -
48D ILE* 2.7 48.0 + - + -
49D GLY 3.4 6.5 + - - -
50D VAL* 5.1 0.2 - - - -
70D LEU* 3.6 30.9 - - + +
79D ALA 3.6 22.7 - - - -
80D TYR 3.9 13.5 + - - -
81D MET* 3.8 21.0 - - + +
94D TYR* 5.3 10.8 - + + -
95D PHE* 3.3 26.5 - - - -
96D CYS* 3.7 10.5 - - + -
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Residues in contact with ILE 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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35D HIS* 5.3 2.7 - - + -
36D TRP* 1.3 74.7 - - - +
38D LYS* 1.3 59.8 + - - +
45D LEU* 3.4 23.1 - - + -
46D GLU 3.3 14.6 - - - +
47D TRP* 3.4 33.4 - - + +
48D ILE* 4.3 1.1 - - - +
93D VAL 3.9 0.3 - - - +
94D TYR* 3.5 8.2 - - - +
95D PHE* 3.0 48.8 + - + +
97D ALA* 5.8 4.9 - - + +
105D TRP* 3.0 40.4 - - + -
180D PRO* 5.7 0.4 - - + -
234D PHE* 4.3 11.7 - - + -
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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 ILE* 1.3 73.4 - - - +
39D GLN* 1.3 60.0 + - - +
40D ARG 4.1 1.6 + - - -
45D LEU* 3.6 2.2 - - - +
46D GLU* 2.8 46.6 + - + +
48D ILE* 4.2 12.4 - - + +
64D PHE* 5.7 3.4 - - + -
92D ALA* 4.7 4.5 - - + -
93D VAL 3.7 4.0 - - - -
94D TYR* 3.6 31.9 - - + +
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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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37D ILE 4.1 0.4 + - - -
38D LYS* 1.3 76.0 - - - +
40D ARG* 1.3 61.7 + - - +
41D PRO* 4.0 6.5 - - + +
44D GLY 3.5 15.3 - - - +
45D LEU* 4.5 16.3 - - + +
92D ALA* 3.6 3.7 - - - +
93D VAL* 2.7 54.0 + - + +
95D PHE* 3.2 29.4 - - + -
174D GLN* 3.2 35.9 + - - +
180D PRO* 4.7 3.3 - - - +
223D PHE* 6.0 1.4 - - - -
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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 4.1 1.6 + - - -
39D GLN* 1.3 74.3 - - - +
41D PRO* 1.3 64.5 - - + +
42D GLY* 4.3 1.8 - - - +
43D GLN* 2.8 24.9 + - + +
44D GLY* 2.7 39.4 + - - +
89D ASP 5.9 1.8 - - - +
91D SER 4.3 7.9 - - - +
92D ALA* 3.9 14.5 - - + +
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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