Contacts of the strand formed by residues 3 - 19 (chain A) in PDB entry 5HJD
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 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.2 31.8 - - - +
2A ALA* 1.3 74.8 - - - +
4A SER* 1.3 65.8 + - - +
126A ASN* 3.9 0.7 - - - +
7C VAL* 5.6 0.2 - - - -
8C GLN 3.2 14.4 - - - -
9C VAL* 4.1 4.7 - - - -
10C LYS* 5.2 1.5 - - - +
135C LEU 3.2 22.2 + - - -
136C LEU* 3.4 21.7 + - - +
138C ALA 2.9 19.3 + - - -
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Residues in contact with SER 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 1.3 77.2 - - - +
5A CYS* 1.3 61.1 + - - +
6A ALA 4.1 0.2 + - - -
126A ASN* 3.3 20.6 - - - -
6C ALA 3.4 3.3 - - - +
7C VAL* 4.5 0.7 - - - -
8C GLN* 3.0 49.4 + - - +
136C LEU* 3.9 6.1 - - - +
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Residues in contact with CYS 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 1.3 74.7 - - - +
6A ALA* 1.3 62.0 + - - +
7A VAL* 3.7 15.5 - - - -
124A PHE 3.6 0.5 - - - +
125A ASN* 3.6 3.7 - - - +
126A ASN* 2.8 40.3 + - - +
127A PRO* 4.4 0.4 - - + +
5C CYS* 2.0 48.0 - - - -
6C ALA 3.4 4.7 - - - -
7C VAL* 4.0 10.1 - - + -
132C ARG* 3.9 18.2 - - - +
136C LEU* 4.2 8.6 - - + +
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Residues in contact with ALA 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER 4.1 0.4 + - - -
5A CYS* 1.3 74.3 - - - +
7A VAL* 1.3 62.6 + - - +
8A GLN* 3.6 9.1 + - + +
123A THR* 4.1 19.1 - - + -
124A PHE 3.5 4.7 - - - -
125A ASN* 4.2 8.1 - - - +
4C SER* 3.5 3.8 + - - +
6C ALA* 3.2 34.0 + - + +
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Residues in contact with VAL 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A CYS* 3.7 24.0 - - - -
6A ALA* 1.3 71.4 - - - +
8A GLN* 1.3 66.8 + - - +
9A VAL* 4.7 1.8 - - + -
122A LEU 3.6 1.0 - - - +
123A THR* 3.6 1.2 - - - -
124A PHE* 2.8 44.7 + - + +
127A PRO* 4.0 20.2 - - + -
132A ARG* 4.0 12.8 - - + -
135A LEU* 3.8 37.0 - - + -
136A LEU* 4.3 13.0 - - + -
4C SER 3.2 10.1 - - - +
5C CYS* 4.1 5.6 - - + -
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Residues in contact with GLN 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ALA* 4.1 11.2 - - + +
7A VAL* 1.3 76.0 - - - +
9A VAL* 1.3 63.5 + - - +
121A LYS* 3.2 40.6 + - + +
122A LEU 3.2 6.1 - - - +
123A THR* 3.6 25.6 + - + +
2C ALA* 3.2 27.8 - - + +
4C SER* 3.0 29.2 + - - +
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Residues in contact with VAL 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.7 3.4 - - + -
8A GLN* 1.3 76.9 - - - +
10A LYS* 1.3 64.8 + - - +
11A LEU* 5.3 0.2 - - + -
47A PHE* 4.1 24.7 - - + -
121A LYS* 3.9 3.7 - - - +
122A LEU* 3.0 56.7 + - + +
124A PHE* 3.7 15.3 - - + -
135A LEU* 3.8 39.3 - - + +
2C ALA 3.2 17.0 - - - +
3C SER 4.3 0.2 - - - +
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Residues in contact with LYS 10 (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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9A VAL* 1.3 78.0 - - - +
11A LEU* 1.3 70.7 + - - +
12A GLU* 6.0 1.1 - - + -
38A GLY* 4.2 1.6 - - - -
39A PRO* 3.4 44.0 - - + +
44A ILE* 4.6 3.3 - - - +
47A PHE* 5.3 0.3 - - - -
120A GLU 3.9 4.5 - - - +
121A LYS* 5.1 12.2 - - + +
1C MET* 3.5 33.6 - - - +
2C ALA* 3.8 20.1 + - + +
119G CYS* 6.4 2.0 - - - -
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Residues in contact with LEU 11 (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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9A VAL* 4.0 0.4 + - + -
10A LYS* 1.3 84.2 - - - +
12A GLU* 1.3 62.1 + - - +
13A LEU* 4.2 5.6 - - + -
36A VAL* 4.7 7.6 - - + -
37A ARG 3.9 12.3 - - - +
44A ILE* 4.1 25.8 - - + -
47A PHE* 4.2 12.3 - - + -
48A VAL* 5.2 0.9 - - + -
87A VAL* 4.2 33.0 - - + -
89A PHE* 5.3 0.7 - - + -
100A PHE* 4.4 9.6 - - + -
119A CYS* 3.6 3.3 - - - +
120A GLU* 2.8 50.4 + - + +
122A LEU* 3.6 32.1 - - + -
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Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS* 5.7 1.3 - - + -
11A LEU* 1.3 79.3 - - - +
13A LEU* 1.3 63.5 + - - +
35A PHE* 3.9 0.7 - - - +
36A VAL* 3.4 5.7 - - - +
37A ARG* 2.8 71.8 + - + +
38A GLY 3.1 19.6 - - - +
39A PRO* 3.5 25.7 - - + +
40A GLU 4.7 1.6 + - - -
117A LEU* 4.2 12.2 - - + +
118A ARG 3.7 2.9 - - - -
119A CYS* 3.8 15.7 - - - -
118G ARG* 5.1 2.9 - - - +
119G CYS* 3.5 22.5 + - - -
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.6 4.7 - - + -
12A GLU* 1.3 82.2 - - - +
14A GLY* 1.3 54.9 + - - +
35A PHE 3.6 5.2 - - - +
36A VAL* 4.2 14.8 - - + -
85A ILE* 3.9 23.3 - - + -
100A PHE* 3.8 42.6 - - + -
102A TYR* 3.8 21.3 - - + -
117A LEU* 3.5 4.4 - - - +
118A ARG* 2.6 53.6 + - + +
120A GLU* 3.7 33.7 - - + -
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Residues in contact with GLY 14 (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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13A LEU* 1.3 74.5 - - - +
15A HIS* 1.3 61.3 + - - +
34A VAL* 3.5 4.0 - - - +
35A PHE* 2.9 52.9 + - - -
102A TYR* 3.1 15.7 - - - -
116A HIS 3.2 11.4 - - - -
117A LEU* 4.3 0.4 - - - -
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Residues in contact with HIS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY* 1.3 75.9 - - - +
16A ARG* 1.3 63.4 + - - +
17A ALA* 4.0 14.1 - - + -
32A TRP* 5.2 0.9 - - + -
33A MET 3.1 13.5 - - - +
34A VAL* 3.9 9.4 - - + -
35A PHE* 3.8 5.9 - - - -
102A TYR* 2.7 35.1 + + + +
103A ASP 3.9 6.5 - - - -
104A LEU* 4.1 16.4 - - + -
105A PHE* 2.8 58.8 + + - -
114A VAL* 3.3 14.4 - - + +
115A ASN* 3.8 2.4 - - - -
116A HIS* 3.1 31.2 + - + +
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Residues in contact with ARG 16 (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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15A HIS* 1.3 72.5 - - - +
17A ALA* 1.3 61.1 + - - +
18A GLN* 6.5 0.2 - - + -
31A ASP 4.6 0.2 - - - -
32A TRP* 3.1 5.8 - - - +
33A MET* 2.8 69.2 + - + +
35A PHE* 5.9 2.5 - - + -
72A LYS* 5.8 2.0 - - - +
114A VAL 3.2 8.5 - - - +
115A ASN* 3.3 27.1 - - + +
112G PRO* 5.6 9.7 - - - +
113G PRO 5.6 5.7 + - - -
115G ASN* 4.4 23.6 + - - +
204G SO4 3.9 21.8 + - - -
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Residues in contact with ALA 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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15A HIS* 4.0 3.4 - - + -
16A ARG* 1.3 75.1 - - - +
18A GLN* 1.3 60.2 + - - +
19A VAL* 4.3 1.0 + - - +
30A HIS* 4.9 3.9 - - + -
31A ASP 3.4 4.9 - - - +
32A TRP* 3.9 3.6 - - + -
105A PHE 3.9 4.7 - - - +
106A LEU* 3.6 32.3 - - + -
107A HIS* 5.3 0.7 + - - +
113A PRO* 3.7 3.1 - - - +
114A VAL* 2.8 57.0 + - + +
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Residues in contact with GLN 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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16A ARG* 4.2 0.6 - - + -
17A ALA* 1.3 75.2 - - - +
19A VAL* 1.3 90.8 + - - +
20A ARG* 5.4 0.2 - - - -
21A LYS* 6.0 3.7 - - - +
30A HIS* 3.3 4.7 - - - -
31A ASP* 2.5 53.9 + - + +
111A HIS 5.6 0.7 - - - +
113A PRO* 3.3 34.8 - - + +
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Residues in contact with VAL 19 (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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17A ALA 4.3 1.1 + - - +
18A GLN* 1.3 95.6 + - - +
20A ARG* 1.3 76.0 + - - +
21A LYS* 3.7 6.8 + - - +
29A THR* 3.8 13.5 - - - +
30A HIS* 3.3 28.9 - - + +
107A HIS 3.8 9.6 - - - +
108A LEU 4.2 10.8 - - - +
109A GLU* 4.2 26.9 - - + +
111A HIS 5.5 4.0 - - - +
113A PRO* 6.3 1.8 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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