Contacts of the strand formed by residues 16 - 28 (chain A) in PDB entry 4HJ5
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 ARG 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A SER 5.2 12.5 + - - +
15A GLN* 1.3 82.3 + - - +
17A CYS* 1.3 64.5 + - - +
18A SER* 5.2 2.4 + - - -
93A ASN* 3.3 41.3 + - - +
94A VAL 3.4 10.1 - - - +
95A ARG* 4.1 10.0 - - - +
116A TYR* 5.7 9.6 - - + -
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Residues in contact with CYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A SER 5.6 0.7 - - - -
6A SER* 4.9 5.8 - - - +
11A ILE* 3.8 24.5 - - + -
15A GLN* 3.8 17.5 - - - +
16A ARG* 1.3 78.4 - - - +
18A SER* 1.3 64.3 + - - +
19A PHE* 4.1 17.3 - - - -
93A ASN* 2.9 20.0 + - - -
94A VAL* 2.9 24.8 + - - +
96A THR* 3.7 29.6 - - - -
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Residues in contact with SER 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A SER 4.0 16.9 + - - -
5A PHE* 3.5 18.7 - - - -
6A SER* 3.0 27.6 + - - +
16A ARG* 5.2 1.6 + - - -
17A CYS* 1.3 72.6 + - - +
19A PHE* 1.3 69.1 + - - +
91A MET 3.0 11.2 - - - -
92A LYS* 3.3 9.1 - - - +
93A ASN* 2.8 31.5 + - - -
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Residues in contact with PHE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 3.8 9.0 - - - -
6A SER 3.4 17.9 - - - +
8A LEU* 3.8 31.4 - - + -
11A ILE* 4.8 4.5 - - + -
17A CYS* 4.1 17.0 - - - -
18A SER* 1.3 79.5 - - - +
20A TYR* 1.3 74.9 + - - +
21A ALA* 3.9 16.4 - - + -
37A VAL* 4.1 9.6 - - + -
39A ASP* 5.6 0.4 - - - +
67A ILE* 4.9 3.8 - - + -
69A CYS* 4.8 5.4 - - - -
89A VAL 4.0 0.2 - - - +
90A VAL* 3.5 2.5 - - - +
91A MET* 2.8 73.9 + - + -
94A VAL* 3.9 20.2 - - + -
96A THR* 5.9 0.2 - - + -
106A CYS* 4.8 5.6 - - + -
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Residues in contact with TYR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 3.6 48.4 - + + +
6A SER 5.0 0.8 + - - -
19A PHE* 1.3 80.3 - - - +
21A ALA* 1.3 65.7 + - - +
39A ASP* 3.7 17.2 - - - +
89A VAL 3.5 2.2 - - - -
90A VAL* 3.8 24.2 - - + +
92A LYS* 5.8 0.2 - - - -
123A VAL* 4.1 18.4 - - + -
129A GLU* 3.7 44.6 + - + +
130A LEU* 4.2 17.9 - - + -
133A ILE* 4.7 7.7 - - + +
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.3 2.0 - - + -
19A PHE* 3.9 12.8 - - + -
20A TYR* 1.3 77.8 - - - +
22A GLN* 1.3 61.7 + - - +
37A VAL* 3.6 29.8 - - + -
38A THR 3.5 14.6 - - - +
39A ASP* 4.6 1.8 - - - +
88A TYR* 3.3 8.9 - - - +
89A VAL* 2.8 43.7 + - + +
130A LEU* 5.2 1.4 - - - +
133A ILE* 5.0 3.6 - - - -
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA* 1.3 73.5 - - - +
23A VAL* 1.3 68.1 + - - +
24A ILE* 3.5 7.1 + - + +
37A VAL* 3.1 4.3 - - - -
38A THR* 2.7 45.1 + - + +
40A TYR* 3.9 22.2 + - - -
86A GLY* 3.2 26.6 + - - +
87A ASP 3.5 10.5 - - - +
88A TYR* 3.6 37.2 + - + -
133A ILE* 4.5 8.5 - - + +
137A LYS* 4.3 11.0 - - - +
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLN* 1.3 72.8 - - - +
24A ILE* 1.3 62.8 + - - +
25A LYS 3.9 7.4 - - - +
26A THR* 3.7 30.3 - - + -
35A LEU* 4.8 5.2 - - + -
36A TYR 3.8 4.9 - - - +
37A VAL* 3.9 17.0 - - + -
83A ILE* 3.9 23.6 - - + -
84A LYS 3.9 7.6 - - - +
85A GLU* 3.9 9.4 - - - -
86A GLY* 2.6 32.1 + - - -
87A ASP 2.7 21.7 + - - +
89A VAL* 4.3 14.8 - - + -
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Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLN* 3.5 12.1 + - + +
23A VAL* 1.3 77.6 - - - +
25A LYS* 1.3 56.9 + - - +
36A TYR 2.8 14.0 + - - +
37A VAL* 4.7 0.2 - - - -
38A THR* 3.6 35.0 - - + +
40A TYR* 4.0 11.2 - - + +
58A TRP* 3.5 27.8 - - + -
59A ARG* 4.0 20.1 + - + +
60A GLY* 3.5 39.7 - - - +
61A PRO* 4.3 2.7 - - + -
66A SER* 4.6 3.6 - - - +
85A GLU* 3.5 19.2 - - - +
86A GLY 5.0 0.2 + - - -
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Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 3.7 1.4 - - - +
24A ILE* 1.3 82.4 - - - +
26A THR* 1.3 78.3 + - - +
27A TRP* 4.7 0.2 - - - -
35A LEU* 3.5 3.5 - - - -
36A TYR* 2.9 50.9 + - + +
58A TRP* 3.7 32.8 - - + -
85A GLU* 3.2 12.8 - - - +
6B C 4.5 8.7 - - - -
7B G 2.7 47.7 + - - -
8B G 3.0 27.5 + - - -
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Residues in contact with THR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 3.7 20.0 - - + -
25A LYS* 1.3 88.6 + - - +
27A TRP* 1.3 68.9 + - - +
28A TYR* 6.2 0.2 - - - -
33A PHE* 3.9 14.2 - - + -
34A THR 3.4 5.6 - - - -
35A LEU* 3.9 13.2 - - + -
36A TYR* 5.5 0.7 - - - -
83A ILE 3.7 20.8 + - - +
84A LYS* 5.2 0.9 - - - -
85A GLU* 3.0 28.8 + - - +
8B G 5.5 1.7 - - - -
9B T 4.2 7.9 + - - +
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Residues in contact with TRP 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS* 5.0 2.0 - - - -
26A THR* 1.3 81.0 - - - +
28A TYR* 1.3 70.8 + - - +
29A SER* 4.1 10.3 + - - -
32A ASN* 4.2 0.9 - - - +
33A PHE* 3.8 3.8 - - - -
34A THR* 2.9 48.7 + - + -
36A TYR* 5.3 0.7 - - + -
7B G 3.3 84.4 - + - +
8B G 3.4 28.3 - + - -
9B T 3.2 57.9 - + + -
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Residues in contact with TYR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR* 6.2 0.2 - - - -
27A TRP* 1.3 79.9 + - - +
29A SER* 1.3 65.9 + - - +
32A ASN 4.1 1.6 - - - +
33A PHE* 3.9 22.6 - + + -
76A ASP* 6.0 0.2 - - - +
80A ARG* 4.9 19.5 - - + +
81A ASN* 6.0 5.2 - - - -
9B T 2.8 118.0 + + + +
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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