Contacts of the strand formed by residues 17 - 23 (chain D) in PDB entry 4YC6
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 PHE 17 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D ASP* 3.2 5.2 - - - +
14D ASP* 3.2 31.1 + - - +
16D GLU* 1.3 90.1 - - + +
18D GLU* 1.3 63.6 + - - +
19D TYR* 3.4 32.5 - - + -
70D ARG* 3.3 57.4 - - + -
71D ARG 3.6 3.1 - - - +
72D PRO* 3.6 35.4 - - + -
73D LEU* 3.8 7.3 - - - +
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Residues in contact with GLU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE 4.9 1.0 - - - +
95A PRO* 4.3 5.2 - - - +
96A PRO* 3.3 35.2 - - + +
11D LYS* 3.7 23.1 + - + +
12D TYR 3.5 9.2 - - - +
13D ASP* 3.8 2.7 - - + +
17D PHE* 1.3 74.4 - - - +
19D TYR* 1.3 62.7 + - - +
54D TRP* 3.6 17.9 - - + -
70D ARG* 3.1 3.1 - - - -
71D ARG* 2.7 80.1 + - + +
72D PRO 5.0 0.7 - - - +
73D LEU* 3.7 13.4 - - + +
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Residues in contact with TYR 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C THR 4.3 5.0 + - - -
241C PHE 4.3 0.9 + - - -
242C PRO* 3.5 25.9 - - + +
243C LYS* 5.4 0.9 - - - +
11D LYS* 3.3 6.9 - - - +
12D TYR* 2.7 66.9 + + + +
13D ASP* 4.1 5.2 - - - -
14D ASP* 2.6 39.1 + - - -
17D PHE* 3.4 28.1 - - + -
18D GLU* 1.3 76.9 - - - +
20D ARG* 1.3 64.7 + - - +
54D TRP* 3.7 5.8 - - - -
57D TYR* 3.3 41.7 - + - -
69D PHE 3.2 5.4 - - - +
70D ARG* 3.7 21.9 + - + -
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Residues in contact with ARG 20 (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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92A ASP* 2.8 38.8 + - - -
8D TYR* 4.5 17.7 - - - +
9D SER* 3.5 28.7 + - - +
10D ASP 3.8 6.3 - - - +
11D LYS* 3.5 28.9 - - + +
12D TYR* 3.7 12.0 + - - -
19D TYR* 1.3 76.9 - - - +
21D HIS* 1.3 71.8 + - - +
22D VAL* 4.1 10.5 - - + -
49D GLN 5.5 0.6 + - - -
50D GLN* 3.1 37.6 - - - +
54D TRP* 3.8 7.9 - - + +
57D TYR* 5.1 0.2 - - - -
69D PHE* 2.8 32.9 + - + +
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Residues in contact with HIS 21 (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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207C ASP* 3.3 29.9 + - - -
208C SER* 4.8 2.2 - - - -
210C ILE* 5.2 1.5 - - + +
211C ASP* 3.3 31.6 + - + +
214C PHE* 5.0 1.1 - + - -
7D TYR* 4.3 1.0 - + - +
9D SER* 2.8 57.3 + - - -
12D TYR* 2.8 29.4 + + - +
20D ARG* 1.3 76.4 - - - +
22D VAL* 1.3 67.5 + - - +
23D MET* 4.5 9.4 - - + -
66D ILE* 4.0 17.9 - - + -
67D LEU 3.2 13.0 - - - +
68D LEU* 4.0 17.1 - - + +
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Residues in contact with VAL 22 (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 ILE* 3.2 33.9 - - + -
7D TYR 3.3 6.5 - - - +
8D TYR* 3.8 27.6 - - + -
20D ARG* 4.1 7.6 - - - +
21D HIS* 1.3 80.7 - - - +
23D MET* 1.3 62.2 + - - +
24D LEU* 3.7 10.4 + - + -
48D VAL* 4.4 9.6 - - + -
50D GLN* 4.9 1.1 - - - +
65D HIS 3.6 1.2 - - - +
66D ILE* 3.4 2.2 - - - -
67D LEU* 2.8 40.0 + - + +
69D PHE* 3.9 27.4 - - + -
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Residues in contact with MET 23 (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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207C ASP* 3.3 37.7 - - + +
208C SER* 4.6 0.7 - - - -
5D GLN 4.7 0.5 - - - +
6D ILE* 3.6 5.4 - - - -
7D TYR* 2.8 66.2 + - + +
21D HIS* 4.5 3.8 - - + -
22D VAL* 1.3 73.2 - - - +
24D LEU* 1.3 64.1 + - - +
25D PRO* 4.2 0.3 - - - +
65D HIS* 3.8 15.0 - - + +
66D ILE* 4.0 28.3 - - + -
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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