Contacts of the strand formed by residues 3 - 19 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7K VAL* 5.1 1.1 - - - -
8K GLN 3.3 10.1 - - - -
9K VAL* 4.0 6.7 - - - +
135K LEU 2.7 28.4 + - - -
136K LEU* 3.8 19.2 - - - +
138K ALA* 2.9 22.4 + - - +
2N ALA* 1.3 78.3 + - - +
4N SER* 1.3 67.2 + - - +
126N ASN* 4.1 6.9 + - - +
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Residues in contact with SER 4 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K ALA 3.2 2.4 - - - +
7K VAL* 3.2 4.1 - - - +
8K GLN* 2.9 52.1 + - - +
136K LEU* 3.9 6.3 - - - +
2N ALA* 6.0 0.3 - - - +
3N SER* 1.3 78.9 - - - +
5N CYS* 1.3 61.7 + - - +
126N ASN* 3.2 22.2 - - - -
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Residues in contact with CYS 5 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K CYS* 2.0 47.6 - - - -
6K ALA 3.3 8.7 - - - -
7K VAL* 3.4 15.0 - - + -
132K ARG* 3.8 15.7 - - - +
136K LEU* 4.6 2.4 - - + +
4N SER* 1.3 76.4 - - - +
6N ALA* 1.3 59.1 + - - +
7N VAL 3.9 1.1 + - - -
124N PHE 3.4 1.7 - - - +
125N ASN* 3.7 2.4 - - - +
126N ASN* 2.8 35.4 + - - +
127N PRO* 4.1 1.1 - - + +
132N ARG* 2.5 24.7 - - - +
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Residues in contact with ALA 6 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K SER* 3.5 9.2 - - - +
6K ALA* 3.4 26.7 + - + +
5N CYS* 1.3 72.9 - - - +
7N VAL* 1.3 63.9 + - - +
8N GLN* 3.6 14.2 + - + +
123N THR* 4.1 14.6 - - - +
124N PHE 3.4 5.4 - - - -
125N ASN* 4.3 10.3 - - - +
132N ARG* 3.9 2.5 - - - -
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Residues in contact with VAL 7 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K SER* 5.9 0.2 - - - -
4K SER 3.4 6.1 - - - +
6N ALA* 1.3 73.0 - - - +
8N GLN* 1.3 65.5 + - - +
9N VAL* 4.2 1.1 - - + -
122N LEU 3.4 0.7 - - - +
123N THR* 3.0 8.0 - - - -
124N PHE* 2.8 46.4 + - + +
127N PRO* 3.4 28.9 - - + -
132N ARG* 3.2 32.1 - - - +
135N LEU* 3.7 35.2 - - + -
136N LEU* 4.7 7.4 - - + -
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Residues in contact with GLN 8 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K ALA 4.4 0.5 - - - -
3K SER* 3.3 26.7 - - - -
4K SER* 3.3 27.6 + - - +
6N ALA* 4.0 14.6 + - - +
7N VAL* 1.3 78.9 - - - +
9N VAL* 1.3 62.4 + - - +
10N LYS* 5.7 4.3 - - + -
121N LYS* 3.2 43.0 + - - +
122N LEU 3.3 5.8 - - - +
123N THR* 4.5 10.1 + - - -
202N SO4 4.0 6.5 + - - -
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Residues in contact with VAL 9 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K ALA 4.1 5.6 - - - +
3K SER* 4.4 3.1 - - - +
7N VAL* 4.2 2.7 - - + -
8N GLN* 1.3 79.8 - - - +
10N LYS* 1.3 63.2 + - - +
11N LEU* 5.2 0.2 - - + -
47N PHE* 3.8 31.9 - - + -
121N LYS* 3.9 3.7 - - - +
122N LEU* 3.0 52.0 + - + +
124N PHE* 3.9 13.2 - - + -
135N LEU* 3.6 45.8 - - + +
138N ALA* 5.2 1.3 - - + -
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Residues in contact with LYS 10 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K MET* 5.8 2.4 - - - +
2K ALA* 3.5 40.9 + - + +
3K SER 5.2 0.6 - - - +
4K SER* 5.9 2.2 - - - -
8N GLN* 5.7 4.3 - - + -
9N VAL* 1.3 79.6 - - - +
11N LEU* 1.3 71.5 + - - +
38N GLY* 4.2 1.2 - - - -
39N PRO* 3.2 31.5 - - + +
40N GLU* 4.6 6.7 + - - -
42N SER* 4.7 1.4 + - - -
44N ILE* 4.6 2.8 - - - +
47N PHE* 5.4 0.3 - - - -
120N GLU 4.0 4.0 - - - +
121N LYS* 4.8 17.0 - - + +
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Residues in contact with LEU 11 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9N VAL* 4.2 0.8 + - + -
10N LYS* 1.3 83.4 - - - +
12N GLU* 1.3 60.4 + - - +
13N LEU* 4.6 10.8 - - + -
36N VAL* 4.7 7.6 - - + -
37N ARG 3.8 6.7 - - - +
39N PRO* 3.9 4.6 - - - +
44N ILE* 3.6 39.9 - - + -
47N PHE* 4.1 13.9 - - + -
48N VAL* 5.5 0.2 - - + -
87N VAL* 4.5 27.4 - - + -
100N PHE* 5.3 5.6 - - + -
119N CYS* 3.7 2.8 - - - +
120N GLU* 2.8 41.5 + - + +
122N LEU* 3.7 31.0 - - + -
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Residues in contact with GLU 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N LEU* 1.3 74.7 - - - +
13N LEU* 1.3 65.4 + - - +
35N PHE* 4.2 1.8 - - + -
36N VAL* 3.9 1.0 - - - -
37N ARG* 2.8 80.1 + - + +
39N PRO* 3.2 35.4 - - + +
40N GLU 4.5 0.9 + - - -
117N LEU* 3.5 28.4 - - + +
118N ARG 3.4 9.4 - - - +
119N CYS* 4.6 7.0 - - + -
117Q LEU* 5.2 7.4 + - + +
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Residues in contact with LEU 13 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N LEU* 4.6 6.1 - - + -
12N GLU* 1.3 83.6 - - - +
14N GLY* 1.3 56.3 + - - +
35N PHE* 3.4 7.4 - - - +
36N VAL* 3.7 27.6 - - + -
85N ILE* 3.8 24.7 - - + -
87N VAL* 6.0 0.4 - - + -
100N PHE* 4.0 36.1 - - + -
102N TYR* 3.8 18.4 - - + -
117N LEU* 3.8 1.5 - - - +
118N ARG* 2.7 56.4 + - + +
120N GLU* 4.4 21.3 - - + -
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Residues in contact with GLY 14 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13N LEU* 1.3 75.1 - - - +
15N HIS* 1.3 60.8 + - - +
34N VAL* 3.3 2.1 - - - +
35N PHE* 2.7 61.5 + - - +
102N TYR* 3.1 11.6 - - - -
116N HIS 3.4 10.3 - - - -
117N LEU* 4.0 1.1 - - - -
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Residues in contact with HIS 15 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N GLY* 1.3 76.3 - - - +
16N ARG* 1.3 61.6 + - - +
17N ALA* 4.3 7.6 - - + -
32N TRP* 5.0 1.6 - - + -
33N MET 3.1 14.6 - - - +
34N VAL* 3.7 17.0 - - + -
35N PHE* 3.9 4.6 - - - -
102N TYR* 2.9 27.1 + + - +
103N ASP 3.9 5.4 - - - -
104N LEU* 3.9 17.0 - - + -
105N PHE* 2.9 57.0 + - + -
114N VAL* 3.3 13.8 - - + +
115N ASN* 3.8 1.8 + - - -
116N HIS* 3.0 38.1 + + + +
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Residues in contact with ARG 16 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15N HIS* 1.3 74.9 - - - +
17N ALA* 1.3 61.0 + - - +
18N GLN* 3.8 3.7 + - + +
32N TRP* 3.8 1.6 - - - -
33N MET* 3.2 49.4 + - + +
35N PHE* 4.7 19.5 - - + -
37N ARG* 5.0 10.1 - - - +
114N VAL 3.2 9.0 - - - +
115N ASN* 3.2 29.2 + - - +
112Q PRO* 5.8 5.1 - - - +
113Q PRO* 5.6 7.5 - - - +
115Q ASN* 6.2 2.4 - - - +
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Residues in contact with ALA 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N HIS* 4.2 2.4 - - + -
16N ARG* 1.3 70.6 - - - +
18N GLN* 1.3 64.3 + - - +
19N VAL* 4.8 3.8 - - - +
30N HIS* 5.3 2.2 - - + +
31N ASP 3.8 6.3 - - - +
32N TRP* 3.8 13.9 - - + -
105N PHE 3.8 4.5 - - - +
106N LEU* 3.6 30.5 - - + -
113N PRO* 4.0 3.3 - - - +
114N VAL* 3.0 45.4 + - + +
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Residues in contact with GLN 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16N ARG* 3.8 4.5 + - + +
17N ALA* 1.3 76.3 - - - +
19N VAL* 1.3 87.6 + - - +
30N HIS* 3.4 4.9 - - - +
31N ASP* 2.8 37.9 + - - +
113N PRO* 3.4 34.5 - - - +
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Residues in contact with VAL 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N ALA 4.8 3.8 - - - +
18N GLN* 1.3 95.8 + - - +
20N ARG* 1.3 78.7 + - - +
21N LYS* 3.5 7.8 + - - +
29N THR 3.8 11.4 - - - +
30N HIS* 3.5 29.4 - - + +
31N ASP* 3.8 2.0 - - - -
107N HIS 5.2 0.4 - - - +
108N LEU 5.0 9.6 - - - +
109N GLU* 5.4 11.4 - - + +
113N PRO* 6.0 3.4 - - + -
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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