Contacts of the helix formed by residues 15 - 26 (chain U) in PDB entry 3H1I
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 ASP 15 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166Q ASN* 3.4 25.2 + - - +
178Q THR* 4.1 4.4 - - - -
179Q MET* 3.2 32.8 - - - +
180Q SER* 3.1 13.7 + - - -
13U LEU 4.0 2.0 + - - -
14U VAL* 1.3 73.6 - - - +
16U PRO* 1.3 60.7 - - - +
17U LEU* 2.5 46.6 + - - +
18U THR* 2.8 35.3 + - + +
19U THR 3.5 2.3 + - - -
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Residues in contact with PRO 16 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178Q THR* 3.9 14.1 - - + +
180Q SER* 3.8 11.4 - - - +
14U VAL* 3.2 11.9 - - + +
15U ASP* 1.3 86.2 - - - +
17U LEU* 1.3 64.5 + - - +
19U THR* 3.5 9.5 + - - +
20U ILE* 3.1 29.9 + - + +
73U LEU* 4.4 7.0 - - + -
76U LYS* 3.9 37.9 - - + +
77U LEU* 4.2 15.9 - - + -
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Residues in contact with LEU 17 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128Q PHE* 5.9 0.2 - - + -
132Q THR* 4.6 9.4 - - + +
179Q MET* 4.6 17.3 - - - -
180Q SER* 4.1 11.7 - - - -
15U ASP* 2.5 31.5 + - - +
16U PRO* 1.3 79.2 - - - +
18U THR* 1.3 70.2 + - + +
20U ILE* 3.0 2.2 + - - +
21U ARG* 3.0 70.2 + - - +
69U VAL* 4.0 7.4 - - + +
73U LEU* 3.4 32.9 - - + +
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Residues in contact with THR 18 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14U VAL* 4.5 6.6 - - - +
15U ASP* 2.8 32.8 + - + +
17U LEU* 1.3 82.2 - - + +
19U THR* 1.3 59.0 + - - -
21U ARG* 3.5 11.7 + - - +
22U GLU* 3.2 29.5 + - - +
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Residues in contact with THR 19 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14U VAL* 3.7 22.0 - - - +
15U ASP 3.5 1.2 + - - -
16U PRO* 3.8 13.2 - - + -
17U LEU 3.1 0.8 + - - -
18U THR* 1.3 80.9 + - - +
20U ILE* 1.3 67.6 + - + +
22U GLU* 3.1 35.8 + - - +
23U HIS* 3.1 9.9 + - + +
76U LYS* 4.8 13.7 - - + +
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Residues in contact with ILE 20 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16U PRO* 3.1 18.8 + - + +
17U LEU* 3.0 4.0 + - - +
19U THR* 1.3 78.8 - - + +
21U ARG* 1.3 60.9 + - - +
22U GLU 3.1 1.6 - - - -
23U HIS* 3.9 13.7 - - + -
24U CYS* 2.9 40.6 + - - +
69U VAL* 4.4 14.6 - - + -
72U LYS* 4.3 24.9 - - + +
73U LEU* 3.9 28.9 - - + +
76U LYS* 4.4 25.6 - - + +
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Residues in contact with ARG 21 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132Q THR* 3.8 31.5 + - - -
133Q GLY* 4.1 3.6 + - - +
134Q TYR 4.9 7.5 + - - -
135Q CYS* 6.2 0.2 - - - +
17U LEU* 3.0 60.2 + - + +
18U THR* 3.9 11.0 - - - +
19U THR 3.3 0.2 - - - -
20U ILE* 1.3 75.2 - - - +
22U GLU* 1.3 59.6 + - - +
24U CYS* 3.8 1.2 - - - +
25U GLU* 2.9 42.1 + - - +
65U ARG* 3.6 45.4 - - - +
66U ASP* 4.6 7.1 + - - -
69U VAL* 3.7 24.5 - - + +
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Residues in contact with GLU 22 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18U THR* 3.2 19.8 + - - +
19U THR* 3.1 28.5 + - - +
21U ARG* 1.3 76.3 - - - +
23U HIS* 1.3 57.7 + - - +
25U GLU* 2.7 37.2 + - - +
26U GLN* 3.3 22.6 + - - +
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Residues in contact with HIS 23 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19U THR* 3.1 12.9 + - + +
20U ILE* 4.0 15.0 - - + +
22U GLU* 1.3 79.8 - - - +
24U CYS* 1.3 61.2 + - - +
26U GLN* 3.6 26.2 + - - +
27U THR* 3.8 8.1 + - - -
72U LYS* 3.7 31.9 + - + +
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Residues in contact with CYS 24 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20U ILE* 2.9 35.0 + - - +
21U ARG* 4.0 5.6 - - - +
23U HIS* 1.3 73.9 - - - +
25U GLU* 1.3 56.5 + - - +
26U GLN 3.0 2.0 - - - -
27U THR* 2.9 15.8 + - - -
30U CYS* 2.7 28.0 - - - -
65U ARG* 4.3 9.0 - - + +
68U CYS* 2.0 54.7 - - + -
69U VAL* 3.5 13.7 - - + -
72U LYS* 4.0 3.8 - - - -
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Residues in contact with GLU 25 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21U ARG* 2.9 33.5 + - - +
22U GLU* 2.7 21.1 + - - +
24U CYS* 1.3 72.5 - - - +
26U GLN* 1.3 61.6 + - - +
27U THR 3.2 0.2 - - - -
30U CYS* 3.2 23.4 - - - +
31U VAL* 3.6 9.7 + - - +
34U ARG* 2.8 37.0 + - + +
61U PHE* 3.9 20.3 - - + -
65U ARG* 4.2 11.6 + - - -
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Residues in contact with GLN 26 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22U GLU* 3.3 30.6 + - - +
23U HIS* 3.6 21.6 + - - +
24U CYS 3.0 0.4 - - - -
25U GLU* 1.3 80.9 - - - +
27U THR* 1.3 65.8 + - - +
28U GLU 3.5 1.2 + - - -
31U VAL* 2.9 16.3 - - - +
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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