Contacts of the strand formed by residues 34 - 42 (chain D) in PDB entry 4UN7
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 SER 34 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D LEU 3.1 13.9 - - - -
28D LYS* 4.0 17.5 - - - +
29D TYR* 4.3 5.3 - - - +
32D ASN 4.9 0.2 - - - -
33D ARG* 1.3 79.1 - - - +
35D GLU* 1.3 62.1 + - - +
36D TYR* 3.8 7.2 - - - -
3F C 3.8 3.4 - - - +
4F G 2.9 51.5 + - - +
5F C 3.1 24.6 + - - -
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Residues in contact with GLU 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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25D TYR 4.4 0.2 - - - -
26D LYS* 3.6 1.7 - - - +
27D LEU* 2.8 38.1 + - + +
29D TYR* 2.5 37.9 + - + +
34D SER* 1.3 76.2 - - - +
36D TYR* 1.3 75.8 + - - +
37D ARG* 2.9 38.5 + - + +
81D ARG* 4.9 1.4 - - - -
83D SER* 2.8 28.4 + - - +
4F G 5.2 0.2 - - - -
5F C 4.2 8.3 - - + -
6F C 3.1 27.7 + - - -
7F G 5.0 0.2 - - - +
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Residues in contact with TYR 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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25D TYR 3.3 4.9 - - - -
26D LYS* 3.9 36.2 + - + -
28D LYS* 4.4 1.2 + - - -
34D SER* 3.8 12.1 + - - -
35D GLU* 1.3 82.4 - - - +
37D ARG* 1.3 63.7 + - - +
82D VAL 3.6 0.2 - - - +
83D SER* 3.4 4.4 + - - -
84D SER 2.8 33.7 + - - +
85D LYS* 3.5 50.7 + - + +
88D TYR* 3.8 25.4 - + + -
89D TYR* 4.0 17.2 + + - -
4F G 2.6 39.0 + - - -
5F C 3.9 9.2 + - - -
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Residues in contact with ARG 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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23D GLY 4.0 0.3 - - - +
24D LEU* 3.5 5.9 - - - -
25D TYR* 2.7 41.6 + - + +
27D LEU* 3.8 17.2 - - + +
29D TYR* 4.1 0.9 - - - -
35D GLU* 2.9 35.9 + - - +
36D TYR* 1.3 76.9 - - - +
38D VAL* 1.3 62.4 + - - +
39D VAL* 4.0 18.2 - - + -
79D GLU* 4.6 0.4 + - - -
81D ARG* 3.4 42.6 - - + +
82D VAL 3.5 4.0 - - - +
83D SER* 4.7 1.8 - - - +
88D TYR* 3.8 5.8 - - - -
17E T 3.7 18.3 + - - -
18E C 3.4 13.3 - - - +
7F G 2.7 29.7 + - - -
8F G 2.8 22.4 + - - -
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Residues in contact with VAL 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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18D ILE* 3.4 34.1 - - + -
23D GLY 3.9 2.7 - - - -
24D LEU* 3.8 8.7 - - + -
37D ARG* 1.3 76.6 - - - +
39D VAL* 1.3 59.3 + - - +
40D ILE* 5.7 0.2 - - + -
56D MET* 4.4 8.5 - - + -
80D LEU* 3.8 1.5 - - - +
81D ARG* 3.4 3.6 - - - -
82D VAL* 2.8 41.7 + - + +
84D SER 4.9 0.2 - - - +
87D LEU* 3.7 24.0 - - + +
88D TYR* 3.7 33.4 - - - +
91D PHE* 3.9 11.4 - - + -
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Residues in contact with VAL 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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18D ILE* 3.9 5.5 - - - +
22D GLY* 3.3 9.9 - - - -
23D GLY 3.1 32.3 + - - +
25D TYR* 3.8 22.7 - - + -
37D ARG* 4.0 13.7 - - + -
38D VAL* 1.3 81.6 - - - +
40D ILE* 1.3 72.3 + - - +
41D THR* 3.9 14.6 - - + -
79D GLU* 3.4 38.4 - - + +
80D LEU 3.3 3.6 - - - +
81D ARG* 4.4 1.8 - - + -
16E T 4.2 12.6 - - + -
17E T 5.6 1.1 - - + +
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Residues in contact with ILE 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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14D LEU* 4.2 4.3 - - + +
17D LEU* 3.7 37.0 - - + +
18D ILE* 3.7 22.0 - - + -
21D ASP* 4.1 5.6 - - + +
22D GLY* 4.1 0.4 - - - -
38D VAL* 5.7 0.2 - - + -
39D VAL* 1.3 80.0 - - - +
41D THR* 1.3 70.1 + - - +
42D GLN* 4.9 2.5 - - + +
48D ILE* 4.2 2.0 - - + +
52D ILE* 3.8 41.3 - - + -
56D MET* 4.3 14.8 - - + -
79D GLU* 3.6 1.4 - - - -
80D LEU* 2.7 52.1 + - + +
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Residues in contact with THR 41 (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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21D ASP* 2.7 28.8 + - - +
22D GLY* 5.1 0.4 - - - -
39D VAL* 3.9 17.3 - - + -
40D ILE* 1.3 78.7 - - - +
42D GLN* 1.3 82.6 + - - +
48D ILE* 4.3 0.9 - - - -
77D ARG* 3.8 27.6 - - - +
78D TYR 3.2 13.2 - - - +
79D GLU* 3.9 8.1 - - + -
14E A 3.2 29.2 - - - +
15E G 3.9 9.2 - - + -
16E T 4.5 1.8 - - + -
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Residues in contact with GLN 42 (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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17D LEU* 6.0 3.0 - - - +
21D ASP* 2.2 37.8 + - - +
40D ILE* 4.9 2.9 - - + +
41D THR* 1.3 83.9 + - - +
43D LYS* 1.3 62.5 + - - +
44D SER* 4.0 12.8 + - - +
47D LEU* 3.9 29.2 - - + +
48D ILE* 3.6 22.3 - - + +
52D ILE* 4.4 9.8 - - + +
77D ARG* 4.3 2.9 - - - -
78D TYR* 2.8 36.3 + - - +
115D VAL* 5.0 5.3 + - - +
116D ALA* 4.9 2.8 - - - +
120D LYS* 5.6 4.5 - - - -
1197D ZN 4.0 0.2 - - - -
14E A 3.2 24.2 + - - -
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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