Contacts of the strand formed by residues 6 - 19 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4K SER* 5.8 1.8 - - - -
5K CYS* 1.3 74.3 - - - +
7K VAL* 1.3 62.3 + - - +
8K GLN* 3.6 9.6 + - + +
123K THR* 4.6 10.8 - - + -
124K PHE 3.4 4.9 - - - -
125K ASN* 4.6 10.8 - - - +
4N SER 3.2 11.3 - - - +
5N CYS* 3.3 13.0 - - - -
6N ALA* 3.4 21.5 + - + +
8N GLN* 6.3 1.6 - - - +
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Residues in contact with VAL 7 (chain K).
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* 3.6 7.9 - - - -
6K ALA* 1.3 71.4 - - - +
8K GLN* 1.3 61.6 + - - +
9K VAL* 4.2 9.0 - - + -
122K LEU 3.5 2.4 - - - +
123K THR* 3.7 1.0 - - - -
124K PHE* 2.9 42.2 + - + +
127K PRO* 3.6 18.2 - - + -
132K ARG* 4.1 13.2 - - + -
135K LEU* 3.6 38.6 - - + -
136K LEU* 4.7 11.0 - - + -
4N SER 3.2 8.7 - - - +
5N CYS* 3.4 23.3 - - + -
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Residues in contact with GLN 8 (chain K).
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* 4.2 11.9 - - + +
7K VAL* 1.3 76.9 - - - +
9K VAL* 1.3 61.2 + - - +
10K LYS* 5.8 0.8 - - + +
121K LYS* 3.3 42.4 + - + +
122K LEU 3.3 7.4 - - - +
123K THR* 4.6 13.1 + - + +
2N ALA 3.7 1.0 - - - +
3N SER* 3.3 25.3 - - - -
4N SER* 2.9 27.0 + - - +
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Residues in contact with VAL 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K VAL* 3.9 4.9 + - + -
8K GLN* 1.3 80.8 - - - +
10K LYS* 1.3 64.6 + - - +
11K LEU* 5.1 0.2 - - + -
47K PHE* 4.0 23.3 - - + -
121K LYS* 3.6 3.6 - - - +
122K LEU* 2.8 47.8 + - + +
124K PHE* 3.5 24.0 - - + -
135K LEU* 3.7 45.1 - - + +
2N ALA 3.8 5.2 - - - +
3N SER* 4.0 3.8 - - - +
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Residues in contact with LYS 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K GLN 5.8 0.4 - - - +
9K VAL* 1.3 79.4 - - - +
11K LEU* 1.3 71.2 + - - +
12K GLU* 6.2 0.9 - - + -
38K GLY* 4.2 1.0 - - - -
39K PRO* 3.5 40.2 - - + +
44K ILE* 4.4 3.6 - - - +
47K PHE* 5.1 0.5 - - - -
119K CYS* 6.3 3.4 - - + -
120K GLU 3.7 5.2 - - - +
121K LYS* 5.0 13.0 - - + -
2N ALA* 3.6 41.0 + - - +
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Residues in contact with LEU 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K VAL* 4.1 0.4 + - + -
10K LYS* 1.3 82.7 - - - +
12K GLU* 1.3 64.9 + - - +
13K LEU* 5.6 2.7 - - + -
36K VAL* 4.7 7.6 - - + -
37K ARG 3.6 14.8 - - - +
44K ILE* 3.8 27.8 - - + -
47K PHE* 4.2 12.3 - - + -
48K VAL* 5.1 0.7 - - + -
87K VAL* 4.3 32.1 - - + -
100K PHE* 4.6 10.5 - - + -
119K CYS* 3.7 2.8 - - - +
120K GLU* 2.8 44.9 + - + +
122K LEU* 3.6 31.4 - - + -
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Residues in contact with GLU 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K LYS* 5.8 0.7 - - + -
11K LEU* 1.3 78.7 - - - +
13K LEU* 1.3 63.3 + - - +
35K PHE* 3.9 0.7 - - - +
36K VAL* 3.4 7.3 - - - +
37K ARG* 2.6 85.8 + - + +
38K GLY 3.2 18.1 - - - +
39K PRO* 3.7 19.8 - - + +
117K LEU* 4.2 12.6 - - + +
118K ARG 3.6 2.7 - - - -
119K CYS* 4.1 22.6 - - - -
118T ARG* 5.2 1.9 - - - +
119T CYS* 4.4 10.9 + - - +
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Residues in contact with LEU 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K LEU* 5.6 2.7 - - + -
12K GLU* 1.3 76.6 - - - +
14K GLY* 1.3 55.6 + - - +
35K PHE 3.7 3.1 - - - +
36K VAL* 3.6 29.6 - - + -
85K ILE* 3.8 20.9 - - + -
87K VAL* 5.7 0.4 - - + -
100K PHE* 3.7 37.9 - - + -
102K TYR* 3.8 17.3 - - + -
117K LEU* 3.6 4.0 - - - +
118K ARG* 2.6 58.1 + - + +
120K GLU* 3.7 30.7 - - + -
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Residues in contact with GLY 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K LEU* 1.3 76.0 - - - +
15K HIS* 1.3 61.1 + - - +
34K VAL* 3.5 3.5 - - - +
35K PHE* 2.8 52.9 + - - -
102K TYR* 3.1 13.6 - - - -
116K HIS 3.2 13.9 - - - -
117K LEU* 4.4 0.2 - - - -
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Residues in contact with HIS 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K GLY* 1.3 75.0 - - - +
16K ARG* 1.3 73.5 + - - +
17K ALA* 4.2 2.9 - - + -
32K TRP* 5.2 0.9 - - + -
33K MET 3.1 14.1 - - - +
34K VAL* 3.9 1.6 - - - -
35K PHE* 3.8 5.9 - - - -
102K TYR* 2.5 35.8 + + + +
103K ASP 4.0 3.4 - - - -
104K LEU* 3.8 29.2 - - + -
105K PHE* 2.9 54.6 + + - -
114K VAL* 3.3 23.8 - - + +
115K ASN* 3.8 2.4 - - - +
116K HIS* 3.1 33.4 + - + +
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Residues in contact with ARG 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K HIS* 1.3 74.2 - - - +
17K ALA* 1.3 60.1 + - - +
18K GLN 4.3 0.4 - - - -
31K ASP 4.6 0.4 - - - -
32K TRP* 3.1 8.2 - - - +
33K MET* 2.8 68.1 + - + +
35K PHE* 6.0 1.8 - - + -
72K LYS* 5.7 1.4 - - - +
74K GLU* 5.6 3.4 + - - -
114K VAL 3.2 7.9 - - - +
115K ASN* 3.3 26.7 - - - +
202K SO4 5.2 2.8 + - - -
112T PRO* 5.3 13.5 - - - +
113T PRO 5.5 5.6 + - - -
115T ASN* 4.3 28.2 + - - +
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Residues in contact with ALA 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K HIS* 4.2 3.1 - - + -
16K ARG* 1.3 74.8 - - - +
18K GLN* 1.3 62.4 + - - +
19K VAL* 4.4 0.5 + - - +
30K HIS* 5.1 3.9 - - + -
31K ASP 3.6 4.3 - - - -
32K TRP* 4.2 2.5 - - + -
105K PHE 4.0 5.2 - - - +
106K LEU* 3.6 33.2 - - + -
107K HIS* 5.2 1.6 + - - +
113K PRO* 3.6 3.6 - - - +
114K VAL* 2.8 54.8 + - + +
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Residues in contact with GLN 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K ARG 4.3 0.2 - - - -
17K ALA* 1.3 73.7 - - - +
19K VAL* 1.3 83.0 + - - +
21K LYS* 5.9 2.6 + - - +
30K HIS* 3.3 8.0 - - - +
31K ASP* 2.8 40.6 + - + +
113K PRO* 3.6 32.6 - - + +
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Residues in contact with VAL 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K ALA 4.4 0.2 + - - -
18K GLN* 1.3 89.9 + - - +
20K ARG* 1.3 77.0 + - - +
21K LYS* 3.7 5.7 + - - -
29K THR* 3.9 12.8 - - - +
30K HIS* 3.3 29.4 - - + +
107K HIS 3.8 9.0 - - - +
108K LEU 4.2 15.5 - - - +
109K GLU* 3.8 29.2 - - + +
111K HIS 5.4 3.8 - - - +
113K PRO* 5.4 1.9 - - + +
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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