Contacts of the helix formed by residues 4 - 19 (chain H) in PDB entry 4PHZ
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 GLU 16 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14J ASN* 5.0 4.9 + - - +
18J GLU* 4.7 0.3 - - - +
17K SER* 1.3 67.2 + - - +
98K ARG* 3.2 38.6 + - - +
102K ARG* 6.5 0.2 - - - -
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Residues in contact with SER 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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18J GLU* 4.7 2.2 - - - -
16K GLU* 1.3 82.8 + - - +
18K VAL* 1.3 65.0 + - - +
19K VAL* 4.1 17.3 - - - -
20K ASP* 4.8 11.2 + - - +
98K ARG* 4.1 1.8 - - - +
102K ARG* 3.7 17.5 - - - +
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Residues in contact with VAL 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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12J PRO 4.3 0.4 - - - +
13J PHE* 4.3 13.0 - - + -
18J GLU* 3.8 11.9 + - + +
22J CYS* 4.2 19.1 - - + -
17K SER* 1.3 72.5 - - - +
19K VAL* 1.3 60.3 + - + +
20K ASP 4.0 1.9 + - - -
98K ARG* 3.5 48.0 - - + +
101K MET* 3.5 38.8 - - + +
102K ARG* 3.3 29.2 - - - +
105K VAL* 4.0 6.5 - - + +
106K VAL* 5.7 0.7 - - - +
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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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18J GLU* 6.1 4.7 - - + +
21J GLY 5.8 1.1 - - - +
22J CYS* 3.9 35.2 - - + +
25J THR* 4.2 22.0 - - + +
26J VAL* 5.0 0.7 - - + -
17K SER* 4.1 11.8 - - - -
18K VAL* 1.3 78.4 - - + +
20K ASP* 1.3 62.8 + - - +
21K LEU* 4.8 8.5 - - + -
105K VAL* 3.8 24.9 - - + -
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Residues in contact with ASP 20 (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 SER* 5.0 11.5 - - - +
18K VAL 4.0 3.6 + - - -
19K VAL* 1.3 74.0 - - - +
21K LEU* 1.3 67.9 + - - +
22K ARG* 3.0 52.5 + - - +
23K GLY 5.6 0.7 - - - -
102K ARG* 6.2 4.0 - - + +
106K VAL* 6.1 4.9 - - + +
109K GLN* 4.6 6.0 - - - +
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Residues in contact with LEU 21 (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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25J THR* 4.7 18.8 - - + +
29J MET* 4.2 18.6 - - + -
19K VAL* 4.8 6.5 - - + -
20K ASP* 1.3 82.9 - - - +
22K ARG* 1.3 66.3 + - - +
23K GLY 3.2 3.1 - - - -
24K MET* 3.1 23.4 + - + +
25K TRP* 3.1 46.6 + - + +
105K VAL* 4.7 4.9 - - + -
109K GLN* 3.3 40.2 + - + +
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Residues in contact with ARG 22 (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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20K ASP* 3.0 44.7 + - - +
21K LEU* 1.3 78.1 - - - +
23K GLY* 1.3 57.9 + - - +
25K TRP* 3.3 37.5 + - - +
26K ILE* 2.9 43.1 + - + +
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Residues in contact with GLY 23 (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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20K ASP* 5.2 1.2 + - - +
21K LEU 3.2 0.8 - - - -
22K ARG* 1.3 75.0 - - - +
24K MET* 1.3 64.5 + - - +
26K ILE* 3.4 13.9 + - - +
27K GLY 3.0 18.2 + - - -
109K GLN* 4.3 1.8 + - - -
302K PGT 3.6 36.6 + - - +
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Residues in contact with MET 24 (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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29J MET* 4.1 24.5 - - + -
21K LEU* 3.1 19.8 + - + +
23K GLY* 1.3 74.4 - - - +
25K TRP* 1.3 92.0 + - + +
27K GLY* 2.9 5.0 + - - -
28K LEU* 2.7 50.2 + - + +
109K GLN* 3.6 33.6 + - + +
112K VAL* 4.0 24.0 - - + -
113K VAL* 4.2 2.6 - - + +
302K PGT 3.6 15.1 - - - +
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Residues in contact with TRP 25 (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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21K LEU* 3.1 38.3 + - + +
22K ARG* 3.3 38.1 - - - +
24K MET* 1.3 102.0 - - + +
26K ILE* 1.3 66.8 + - - +
28K LEU* 4.1 20.4 - - + -
29K VAL* 2.9 36.1 + - + +
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Residues in contact with ILE 26 (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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22K ARG* 2.9 38.8 + - + +
23K GLY* 3.5 11.0 - - - +
24K MET 3.2 0.2 - - - -
25K TRP* 1.3 72.9 - - + +
27K GLY* 1.3 59.0 + - - +
29K VAL* 3.8 3.5 - - - +
30K LEU* 2.8 56.7 + - + +
302K PGT 6.1 1.8 - - + -
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Residues in contact with GLY 27 (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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23K GLY 3.0 10.0 + - - -
24K MET 2.9 11.4 + - - -
26K ILE* 1.3 70.9 - - - +
28K LEU* 1.3 64.3 + - - -
30K LEU* 3.3 4.0 + - - +
31K LEU* 3.0 27.1 + - - +
113K VAL* 4.3 9.2 - - - -
302K PGT 3.6 32.5 - - - +
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Residues in contact with LEU 28 (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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24K MET* 2.7 34.0 + - + +
25K TRP* 3.8 29.8 - - + +
27K GLY* 1.3 70.7 - - - +
29K VAL* 1.3 63.7 + - + +
31K LEU* 3.2 2.5 + - + +
32K ASN* 2.9 41.4 + - - +
112K VAL* 4.4 11.2 - - + -
113K VAL* 3.8 21.1 - - + +
116K ILE* 4.2 37.7 - - + -
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Residues in contact with VAL 29 (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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25K TRP* 2.9 30.2 + - + +
26K ILE* 3.8 3.1 - - - +
28K LEU* 1.3 74.0 - - + +
30K LEU* 1.3 61.0 + - + +
31K LEU 2.8 6.8 + - - -
32K ASN* 4.8 2.5 - - - +
33K VAL* 3.0 42.7 + - + +
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Residues in contact with LEU 30 (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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26K ILE* 2.8 46.0 + - + +
27K GLY* 3.7 6.7 - - - +
29K VAL* 1.3 73.8 - - + +
31K LEU* 1.3 59.6 + - - +
33K VAL* 4.8 4.0 - - - -
34K PHE* 3.5 20.5 - - - +
302K PGT 5.0 20.0 - - + +
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Residues in contact with LEU 31 (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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27K GLY 3.0 15.0 + - - +
28K LEU* 3.7 4.5 - - + +
29K VAL 2.8 2.2 + - - -
30K LEU* 1.3 78.6 - - - +
32K ASN* 1.3 68.5 + - - +
33K VAL 3.1 0.7 - - - -
34K PHE* 2.9 19.7 + - + +
35K TYR* 2.9 33.8 + - + +
113K VAL* 4.4 15.9 - - + +
116K ILE* 3.5 28.0 - - + -
117K ALA* 4.0 22.2 - - + +
156K ILE* 4.2 23.1 - - + -
160K ILE* 4.6 1.3 - - + -
302K PGT 3.9 24.2 - - + -
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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