Contacts of the strand formed by residues 6 - 19 (chain Q) 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 ALA 6 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4Q SER* 6.2 0.9 - - - -
5Q CYS* 1.3 74.9 - - - +
7Q VAL* 1.3 62.6 + - - +
8Q GLN* 3.7 8.5 + - + +
123Q THR* 4.1 18.2 - - + -
124Q PHE 3.6 5.6 - - - -
125Q ASN* 4.2 8.5 - - - +
4T SER 3.4 8.7 - - - +
6T ALA* 3.5 33.4 + - + +
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Residues in contact with VAL 7 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q CYS* 3.6 25.1 - - - -
6Q ALA* 1.3 71.4 - - - +
8Q GLN* 1.3 67.7 + - - +
9Q VAL* 4.7 2.5 - - + -
122Q LEU 3.4 1.6 - - - +
123Q THR* 3.4 1.4 - - - -
124Q PHE* 2.7 41.3 + - - +
127Q PRO* 3.7 18.6 - - + -
132Q ARG* 4.0 12.6 - - + -
135Q LEU* 3.8 37.2 - - + -
136Q LEU* 4.3 12.3 - - + -
4T SER 3.1 11.7 - - - +
5T CYS* 4.2 3.4 - - + -
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Residues in contact with GLN 8 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202N SO4 4.0 3.3 + - - -
6Q ALA* 4.3 8.9 + - - +
7Q VAL* 1.3 76.7 - - - +
9Q VAL* 1.3 63.9 + - - +
10Q LYS* 6.5 0.2 - - + -
121Q LYS* 2.8 38.9 + - + +
122Q LEU 3.2 4.3 - - - +
123Q THR* 3.8 28.1 + - + +
2T ALA 3.5 1.4 - - - +
3T SER* 3.3 26.3 + - - -
4T SER* 3.2 19.9 + - - +
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Residues in contact with VAL 9 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Q VAL* 4.2 3.1 + - + -
8Q GLN* 1.3 80.4 - - - +
10Q LYS* 1.3 67.1 + - - +
11Q LEU* 4.1 0.4 + - + -
47Q PHE* 4.0 24.2 - - + -
120Q GLU 4.0 0.2 - - - +
121Q LYS* 3.4 3.6 - - - +
122Q LEU* 2.8 61.5 + - + +
124Q PHE* 3.9 12.8 - - + -
135Q LEU* 3.7 42.4 - - + +
138Q ALA* 5.1 0.4 - - + -
2T ALA 3.4 9.2 - - - +
3T SER* 4.1 1.1 - - - +
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Residues in contact with LYS 10 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121N LYS* 6.2 1.6 - - - +
202N SO4 4.2 26.5 + - - -
8Q GLN* 6.5 0.2 - - + -
9Q VAL* 1.3 79.5 - - - +
11Q LEU* 1.3 70.7 + - - +
12Q GLU* 6.2 0.4 - - + -
38Q GLY* 4.0 2.1 - - - -
39Q PRO* 3.3 28.5 - - + +
42Q SER* 4.9 0.3 + - - -
44Q ILE* 4.7 2.9 - - - +
119Q CYS* 6.4 1.3 - - + -
120Q GLU 3.5 5.2 - - - +
121Q LYS* 4.5 15.3 - - + +
1T MET 5.3 4.0 + - - -
2T ALA* 3.5 31.6 + - + +
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Residues in contact with LEU 11 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Q VAL* 5.0 0.9 - - + -
10Q LYS* 1.3 82.9 - - - +
12Q GLU* 1.3 68.4 + - - +
13Q LEU* 4.3 3.8 - - + -
36Q VAL* 4.9 7.9 - - + -
37Q ARG 3.5 4.7 - - - +
44Q ILE* 4.0 35.7 - - + -
47Q PHE* 4.2 14.1 - - + -
48Q VAL* 5.2 1.1 - - + -
87Q VAL* 4.3 28.9 - - + -
100Q PHE* 4.5 11.0 - - + -
119Q CYS* 3.6 1.6 - - - +
120Q GLU* 2.7 45.1 + - + +
122Q LEU* 3.6 31.9 - - + -
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Residues in contact with GLU 12 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117N LEU 5.0 1.1 - - - +
118N ARG* 5.0 1.0 - - - +
119N CYS* 3.3 24.3 + - - +
10Q LYS* 6.2 0.2 - - + -
11Q LEU* 1.3 79.7 - - - +
13Q LEU* 1.3 63.1 + - - +
35Q PHE* 3.9 1.1 - - - +
36Q VAL* 3.5 5.5 - - - +
37Q ARG* 2.6 76.0 + - + +
39Q PRO* 3.8 32.4 - - + +
40Q GLU 4.8 1.4 + - - -
117Q LEU* 4.0 19.6 - - + +
118Q ARG 3.6 2.7 - - - -
119Q CYS* 3.8 15.9 - - + -
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Residues in contact with LEU 13 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q LEU* 5.5 3.6 - - + -
12Q GLU* 1.3 75.9 - - - +
14Q GLY* 1.3 56.5 + - - +
35Q PHE* 3.6 4.3 - - - +
36Q VAL* 3.7 32.8 - - + -
85Q ILE* 4.0 16.8 - - + -
87Q VAL* 5.5 0.7 - - + -
100Q PHE* 3.9 33.7 - - + -
102Q TYR* 4.7 13.2 - - + -
117Q LEU* 3.6 4.2 - - - +
118Q ARG* 2.6 77.2 + - + +
120Q GLU* 3.8 20.4 - - + -
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Residues in contact with GLY 14 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Q LEU* 1.3 76.2 - - - +
15Q HIS* 1.3 64.1 + - - +
34Q VAL* 3.4 3.8 - - - +
35Q PHE* 2.9 51.0 + - - -
102Q TYR* 3.5 11.9 + - - -
116Q HIS 3.2 13.2 - - - -
117Q LEU* 4.5 0.2 - - - -
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Residues in contact with HIS 15 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Q GLY* 1.3 76.5 - - - +
16Q ARG* 1.3 73.6 + - - +
17Q ALA* 4.4 1.6 - - + -
33Q MET 3.0 17.0 - - - +
34Q VAL* 4.0 7.2 - - + -
35Q PHE* 3.7 4.6 - - - -
102Q TYR* 2.4 39.4 + + + -
103Q ASP 3.8 6.3 - - - -
104Q LEU* 3.8 20.6 - - + -
105Q PHE* 2.9 58.7 + + - -
114Q VAL* 3.5 7.1 - - + +
115Q ASN* 3.7 2.5 - - - -
116Q HIS* 3.0 38.2 + - + +
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Residues in contact with ARG 16 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107N HIS* 6.0 1.8 - - - -
112N PRO* 6.3 1.2 - - - +
113N PRO 5.5 4.2 + - - -
115N ASN* 2.5 53.0 + - - +
201N SO4 3.7 24.5 + - - -
15Q HIS* 1.3 79.3 - - - +
17Q ALA* 1.3 61.2 + - - +
18Q GLN* 4.3 1.1 - - + +
31Q ASP 4.7 0.4 - - - -
32Q TRP* 3.2 7.4 - - - +
33Q MET* 3.0 55.4 + - + +
35Q PHE* 5.4 8.0 - - + -
114Q VAL 3.1 14.6 - - - +
115Q ASN* 3.8 14.6 + - - +
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Residues in contact with ALA 17 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15Q HIS* 4.4 2.2 - - + -
16Q ARG* 1.3 76.6 - - - +
18Q GLN* 1.3 60.6 + - - +
30Q HIS* 4.7 5.8 - - + -
31Q ASP 3.6 5.6 - - - -
32Q TRP* 4.2 2.5 - - + -
105Q PHE 4.1 3.8 - - - +
106Q LEU* 3.5 34.8 - - + -
107Q HIS* 5.2 1.6 + - - +
113Q PRO* 3.9 3.2 - - - +
114Q VAL* 3.1 49.0 + - + +
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Residues in contact with GLN 18 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Q ARG* 6.4 0.2 - - + -
17Q ALA* 1.3 74.3 - - - +
19Q VAL* 1.3 78.2 + - + +
30Q HIS* 3.2 9.5 - - - +
31Q ASP* 2.9 40.3 + - + +
113Q PRO* 4.8 22.5 - - + +
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Residues in contact with VAL 19 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Q GLN* 1.3 93.5 + - + +
20Q ARG* 1.3 68.9 + - - +
21Q LYS* 5.7 1.4 + - - +
29Q THR* 3.7 10.8 - - + +
30Q HIS* 3.3 31.4 - - + +
31Q ASP* 6.2 0.2 - - - -
107Q HIS 4.2 6.1 - - - +
108Q LEU 4.8 1.3 - - - +
109Q GLU* 4.6 29.8 - - + +
111Q HIS 6.2 0.2 - - - +
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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