Contacts of the helix formed by residues 11 - 17 (chain U) in PDB entry 4IL6
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 ASN 11 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B ARG* 3.4 8.5 - - - +
163O GLY 4.1 3.6 + - - -
164O LEU* 3.2 35.8 + - - +
169O ASP* 6.0 1.2 - - - +
187O VAL* 3.5 14.5 - - + +
188O LYS 4.4 8.7 + - - +
10U VAL* 1.3 77.5 - - - +
12U VAL* 1.3 62.7 + - - +
13U VAL* 2.9 10.4 + - - +
14U ASP* 2.8 46.0 + - + +
15U GLU 3.1 16.5 + - - -
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Residues in contact with VAL 12 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164O LEU* 4.1 16.2 - - + +
188O LYS 5.1 0.4 + - - +
189O ARG* 6.3 2.7 - - + -
190O PHE* 5.5 4.5 - - + +
10U VAL* 3.4 14.5 + - + +
11U ASN* 1.3 71.1 + - - +
13U VAL* 1.3 62.2 + - - +
15U GLU* 3.5 7.0 + - - +
16U LYS* 2.9 29.5 + - - +
88U GLU* 3.4 39.1 - - + +
90U ALA* 4.3 9.2 - - + -
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Residues in contact with VAL 13 (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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385B ARG* 3.7 32.3 - - + -
164O LEU* 3.9 26.9 - - + +
165O ALA* 4.4 12.3 - - + -
11U ASN* 2.9 6.5 + - - +
12U VAL* 1.3 75.4 - - + +
14U ASP* 1.3 65.1 + - - +
16U LYS* 3.2 10.3 + - + +
17U LEU* 3.2 23.6 + - + +
21U TYR* 5.2 5.3 - - + +
88U GLU* 5.3 0.9 - - + -
90U ALA* 4.4 13.9 - - + -
91U LEU* 4.1 31.0 - - + -
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Residues in contact with ASP 14 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PRO* 4.7 3.8 - - - +
385B ARG* 2.7 49.2 + - - -
393B GLU* 3.2 35.5 - - - +
418B LYS* 3.8 18.3 + - - +
169O ASP* 5.3 2.8 - - - +
11U ASN* 2.8 32.4 + - + +
13U VAL* 1.3 72.6 - - - +
15U GLU* 1.3 61.4 + - - +
17U LEU* 3.1 23.4 + - - +
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Residues in contact with GLU 15 (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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393B GLU* 4.9 4.0 - - - -
10U VAL* 3.1 30.1 - - + +
11U ASN 3.1 16.7 + - - +
12U VAL* 3.8 7.0 - - - +
13U VAL 3.3 0.2 - - - -
14U ASP* 1.3 75.4 - - - +
16U LYS* 1.3 64.1 + - - +
18U GLY* 2.9 16.9 + - - +
19U THR* 3.8 9.8 + - + +
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Residues in contact with LYS 16 (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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12U VAL 2.9 15.1 + - - +
13U VAL* 3.2 16.2 - - - +
15U GLU* 1.3 77.8 - - - +
17U LEU* 1.3 53.5 + - - +
18U GLY 3.1 0.2 - - - -
19U THR* 2.7 42.4 + - + +
21U TYR* 3.6 30.6 - - + +
26U ASP* 4.4 0.4 - - - -
29U ASN* 3.6 10.8 - - - +
85U THR* 3.0 26.0 + - - -
86U GLU* 2.7 35.1 + - - +
87U VAL 4.9 0.2 - - - -
88U GLU* 3.9 20.7 + - + +
91U LEU* 4.2 10.1 - - + -
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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
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382B PRO* 4.7 2.7 - - + -
385B ARG* 4.3 14.1 - - + +
388B SER* 4.1 10.8 - - - +
391B SER* 3.8 31.4 - - - +
393B GLU* 3.7 4.3 - - + +
394B GLN* 3.4 32.5 + - + +
627B DMS 3.5 33.9 - - + -
13U VAL* 3.2 15.3 + - + +
14U ASP* 3.1 31.6 + - - +
16U LYS* 1.3 76.8 - - - +
18U GLY* 1.3 57.4 + - - +
19U THR 3.3 2.5 + - - +
21U TYR* 4.0 14.1 - - + -
22U GLY* 3.6 10.6 - - - -
23U GLU* 5.6 0.3 - - - +
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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