Contacts of the helix formed by residues 3 - 19 (chain C) in PDB entry 5ITY
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 3 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C GLY* 1.3 71.7 - - - -
4C GLY* 1.3 69.9 + - - +
5C PRO* 3.2 6.1 - - + -
6C GLU* 2.6 24.5 + - - +
7C LEU* 3.1 16.6 + - - +
54C LYS* 3.8 7.2 - - - -
173C GLY 3.6 7.2 - - - +
175C GLY* 2.6 38.3 + - - +
176C ASN 3.2 1.9 + - - -
177C TYR* 2.8 49.6 + - + -
178C LEU* 3.1 17.5 - - - +
297F CTG 3.1 16.0 + - - +
298F G 3.3 11.0 - - - +
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Residues in contact with GLY 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLU* 1.3 70.0 - - - +
5C PRO* 1.3 66.4 - - - +
7C LEU* 3.2 4.0 + - - +
8C HIS* 3.1 22.1 + - - +
53C GLY* 3.5 19.3 - - - +
54C LYS* 3.9 1.4 - - - +
136C CYS* 6.2 1.3 - - - -
137C VAL* 6.1 1.3 - - - -
138C LEU* 4.6 9.9 - - - +
173C GLY* 2.7 31.4 + - - -
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Residues in contact with PRO 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLU* 3.2 6.3 - - + -
4C GLY* 1.3 90.5 - - - +
6C GLU* 1.3 56.7 + - - +
8C HIS* 3.2 7.6 + - + +
9C LEU* 2.8 41.4 + - + +
138C LEU* 4.6 2.7 - - + -
177C TYR* 3.4 13.2 - - - +
178C LEU* 3.8 23.8 - - + -
233C PRO* 4.1 20.2 - - + +
236C VAL* 3.8 31.2 - - + -
237C VAL* 4.5 8.5 - - + +
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Residues in contact with GLU 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C GLY* 3.9 7.9 - - - -
3C GLU* 2.6 38.4 + - - +
5C PRO* 1.3 78.6 - - - +
7C LEU* 1.3 67.3 + - + +
9C LEU* 3.9 8.7 - - + +
10C ALA* 2.9 24.9 + - - +
79C PHE* 4.9 8.0 - - + -
177C TYR* 2.7 21.4 + - - -
236C VAL* 3.9 3.6 - - - +
242C ARG* 3.2 29.0 + - - +
244C TYR* 4.7 7.2 + - + +
297F CTG 3.3 25.0 - - - +
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Residues in contact with LEU 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C GLY 4.1 9.2 - - - +
3C GLU 3.1 29.6 + - - +
4C GLY 3.2 6.3 + - - +
6C GLU* 1.3 76.1 - - - +
8C HIS* 1.3 52.7 + - - +
10C ALA* 3.0 6.4 + - - +
11C SER* 2.8 34.8 + - - -
51C ALA* 3.9 4.9 - - + -
53C GLY 3.5 7.2 - - - +
54C LYS* 3.6 26.7 - - + -
55C GLU* 3.4 26.9 - - - +
56C LEU* 3.8 21.4 - - + +
77C PHE 4.7 0.9 - - - +
79C PHE* 3.6 43.5 - - + +
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Residues in contact with HIS 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLY 3.1 9.9 + - - +
5C PRO* 3.5 8.7 - - + +
7C LEU* 1.3 79.3 - - - +
9C LEU* 1.3 58.8 + - - +
11C SER* 3.1 5.3 + - - -
12C GLN* 2.8 42.5 + - + +
51C ALA* 3.6 18.9 + - + +
136C CYS* 6.0 0.2 - - - -
138C LEU* 4.1 15.6 - - + +
139C GLN* 2.7 42.5 + - - +
237C VAL* 3.9 25.2 - - + +
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Residues in contact with LEU 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PRO 2.8 27.0 + - - +
6C GLU* 3.9 7.4 - - - +
8C HIS* 1.3 72.5 - - - +
10C ALA* 1.3 52.8 + - - +
12C GLN* 3.1 24.7 + - - +
13C PHE* 2.7 35.6 + - - +
236C VAL* 3.9 28.0 - - + +
237C VAL* 3.9 26.9 - - + +
240C GLY* 4.8 13.5 - - - +
241C GLY 5.6 1.8 - - - +
242C ARG* 5.2 19.7 - - + +
244C TYR* 4.5 17.3 - - + +
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Residues in contact with ALA 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLU 2.9 15.3 + - - +
7C LEU 3.3 8.1 - - - +
9C LEU* 1.3 77.1 - - - +
11C SER* 1.3 62.6 + - - +
13C PHE* 3.0 9.7 + - - +
14C VAL* 2.8 26.7 + - - +
56C LEU* 3.8 16.8 - - + -
79C PHE* 4.1 13.7 - - + -
85C PHE* 4.7 6.5 - - + -
244C TYR* 3.8 23.5 - - + +
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Residues in contact with SER 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU 2.8 10.4 + - - -
8C HIS* 3.2 9.6 - - - -
10C ALA* 1.3 73.9 - - - +
12C GLN* 1.3 58.5 + - - +
14C VAL 3.1 7.1 + - - -
15C ASN* 2.5 25.4 + - - -
49C ALA* 3.4 24.5 + - - +
50C SER* 3.3 23.5 - - - -
51C ALA* 3.6 25.5 + - - -
56C LEU* 3.7 5.7 - - - +
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Residues in contact with GLN 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C HIS* 2.8 30.1 + - + +
9C LEU* 3.3 27.8 - - + +
11C SER* 1.3 72.7 + - - +
13C PHE* 1.3 63.8 + - - +
15C ASN* 3.6 8.3 + - - +
16C GLU* 2.9 60.2 + - - +
237C VAL* 4.4 8.3 - - - +
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Residues in contact with PHE 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU 2.7 17.2 + - - +
10C ALA 3.4 8.7 - - - +
12C GLN* 1.3 74.4 - - - +
14C VAL* 1.3 70.8 + - + +
16C GLU* 3.3 4.2 + - + +
17C ALA* 3.1 34.6 + - + +
85C PHE* 3.7 27.6 - - + -
86C GLN* 4.3 3.6 - - - -
87C LEU* 4.0 28.3 - - + -
112C LEU* 4.7 9.9 - - + -
243C GLY 5.2 1.6 - - - -
244C TYR* 3.4 59.7 - + + +
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Residues in contact with VAL 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ALA 2.8 17.9 + - - +
11C SER 3.1 6.9 + - - +
13C PHE* 1.3 83.5 - - + +
15C ASN* 1.3 68.4 + - - +
17C ALA* 3.9 0.4 - - - -
18C CYS* 3.0 33.7 + - - +
47C ILE* 3.8 29.2 - - + +
48C SER 4.1 6.1 - - - -
49C ALA* 3.7 20.0 - - + -
56C LEU* 5.3 1.3 - - + -
58C LEU* 4.1 5.4 - - + -
85C PHE* 4.3 33.9 - - + -
112C LEU* 4.9 5.6 - - + -
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Residues in contact with ASN 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C SER* 2.5 32.3 + - - -
12C GLN* 3.6 9.3 - - - +
14C VAL* 1.3 76.1 - - - +
16C GLU* 1.3 60.4 + - - +
18C CYS 3.6 0.2 - - - -
19C ARG* 2.8 42.7 + - - +
47C ILE 4.7 5.8 - - - -
48C SER* 3.8 7.1 + - - -
49C ALA 2.9 38.2 + - - +
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Residues in contact with GLU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C GLN* 2.9 58.4 + - - +
13C PHE* 4.0 4.9 - - + +
14C VAL 3.1 0.4 - - - -
15C ASN* 1.3 83.0 + - - +
17C ALA* 1.3 57.6 + - - +
19C ARG* 3.5 40.5 + - - +
20C ALA 5.7 0.2 + - - -
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Residues in contact with ALA 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C PHE* 3.1 32.9 + - + +
14C VAL* 4.6 0.9 - - - +
16C GLU* 1.3 77.5 - - - +
18C CYS* 1.3 62.4 + - - +
19C ARG 3.7 0.4 - - - -
20C ALA* 4.9 2.4 + - - +
21C LEU* 3.3 27.4 + - - +
87C LEU* 3.9 22.4 - - + +
112C LEU* 6.3 0.4 - - + -
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Residues in contact with CYS 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C VAL* 3.0 20.1 + - - +
15C ASN 3.6 0.4 - - - -
17C ALA* 1.3 85.5 - - - +
19C ARG* 1.3 65.9 + - - +
20C ALA 3.2 2.2 - - - -
21C LEU* 3.5 22.2 + - - +
23C PHE* 3.8 31.8 - - + -
46C ARG* 4.4 5.0 - - - +
47C ILE* 3.8 35.2 + - + +
87C LEU* 5.6 1.8 - - - -
112C LEU* 4.1 21.3 - - - -
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Residues in contact with ARG 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ASN* 2.8 19.1 + - - +
16C GLU* 3.5 48.9 + - - +
17C ALA 3.7 0.2 - - - -
18C CYS* 1.3 78.4 - - - +
20C ALA* 1.3 63.3 + - - +
46C ARG* 3.3 23.8 + - - +
47C ILE 5.7 0.2 - - - -
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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
------------------------------------------------------------
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