Contacts of the strand formed by residues 11 - 19 (chain D) in PDB entry 4UQJ
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 11 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ASN* 1.3 71.4 - - - +
12D ILE* 1.3 62.8 + - - +
13D GLN* 3.7 4.2 + - - +
42D ARG* 3.7 4.7 - - - -
44D THR* 3.2 22.0 + - - -
71D TYR* 4.4 10.0 + - - -
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Residues in contact with ILE 12 (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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10D ASN* 4.9 3.4 - - + +
11D SER* 1.3 73.7 + - - +
13D GLN* 1.3 61.2 + - - +
14D ILE* 3.6 14.7 + - + +
41D PHE* 3.9 26.2 - - + -
42D ARG 3.0 14.4 + - - +
43D LEU* 3.5 10.8 - - + -
44D THR* 2.9 24.2 + - - -
71D TYR* 3.7 31.0 - - + -
296D PHE* 3.6 33.2 - - + +
306D ILE* 6.3 3.1 - - + -
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Residues in contact with GLN 13 (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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11D SER* 3.7 5.0 + - - +
12D ILE* 1.3 71.7 - - - +
14D ILE* 1.3 62.5 + - - +
44D THR* 3.5 18.2 - - + +
46D HIS* 6.6 0.2 - - + -
68D ARG 5.4 2.5 - - - +
69D GLY 4.3 15.0 - - - +
70D VAL* 3.4 8.3 - - + -
71D TYR* 3.0 38.8 + - + -
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Residues in contact with ILE 14 (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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12D ILE* 4.1 19.5 - - + +
13D GLN* 1.3 79.7 - - - +
15D GLY* 1.3 64.2 + - - +
29D PHE* 4.6 18.4 - - + -
33D MET* 5.1 1.3 - - - -
43D LEU* 4.1 26.5 - - + -
44D THR 3.0 12.8 + - - +
45D PRO* 3.9 10.5 - - + -
46D HIS* 3.0 28.6 + - - +
70D VAL* 3.8 6.6 - - - +
71D TYR* 5.2 0.4 - - + -
72D ALA* 3.3 22.4 - - + +
74D PHE* 5.8 0.4 - - + -
292D MET* 3.7 33.7 - - + -
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Residues in contact with GLY 15 (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 ILE* 1.3 80.0 - - - +
16D GLY* 1.3 58.8 + - - -
17D LEU* 4.2 0.4 - - - -
29D PHE* 5.6 0.9 - - - -
45D PRO* 5.7 0.4 - - - -
46D HIS* 4.0 6.1 - - - -
65D GLN* 4.6 12.3 - - - -
70D VAL* 3.8 11.2 - - - +
72D ALA 2.9 12.4 + - - -
73D ILE* 4.2 11.2 - - - -
74D PHE* 2.8 29.6 + - - +
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Residues in contact with GLY 16 (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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15D GLY* 1.3 73.9 - - - -
17D LEU* 1.3 65.2 + - - +
18D PHE* 3.6 19.3 + - - -
29D PHE* 5.5 2.7 - - - -
46D HIS 3.1 13.5 + - - +
47D ILE* 3.5 10.4 - - - -
48D ASP* 2.8 30.0 + - - +
74D PHE* 3.1 7.4 - - - -
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Residues in contact with LEU 17 (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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15D GLY* 4.5 1.8 - - - -
16D GLY* 1.3 78.4 - - - +
18D PHE* 1.3 61.9 + - - +
19D PRO* 3.6 2.1 - - - +
48D ASP* 3.7 11.9 - - + +
58D VAL* 4.6 22.4 - - + +
61D ALA* 4.2 37.9 - - + +
62D PHE* 4.8 3.4 - - + +
65D GLN* 5.1 4.0 - - + -
73D ILE* 3.6 24.7 - - + -
74D PHE 2.9 9.5 + - - -
75D GLY* 3.1 26.5 - - - -
76D PHE* 3.3 17.6 + - - +
85D ILE* 4.6 12.3 - - + -
96D PHE* 4.6 7.2 - - + -
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Residues in contact with PHE 18 (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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16D GLY* 3.6 19.3 + - - -
17D LEU* 1.3 75.7 - - - +
19D PRO* 1.3 70.3 - - + +
22D ALA* 4.4 8.3 - - + +
25D GLU 4.0 6.5 - - - -
26D TYR* 3.7 50.3 - + + -
29D PHE* 3.4 21.8 - + + -
47D ILE* 4.1 12.6 - - + -
48D ASP 3.4 6.2 + - - -
49D ASN* 3.3 36.6 - - - +
50D LEU 3.6 3.1 + - - -
74D PHE* 3.3 38.1 - + - -
76D PHE* 3.9 13.9 - + - -
285D THR* 4.4 0.7 - - + -
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Residues in contact with PRO 19 (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 3.6 3.1 - - - +
18D PHE* 1.3 85.9 - - + +
20D ARG* 1.3 69.8 + - - +
21D GLY 3.0 0.2 + - - -
22D ALA* 3.0 28.8 + - + +
49D ASN* 5.7 0.2 - - - -
50D LEU 3.4 11.7 - - - +
52D VAL* 3.7 37.5 - - + +
76D PHE* 3.4 35.9 - - + -
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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