Contacts of the helix formed by residues 3 - 19 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B GLY* 1.3 78.8 - - - +
4B GLY* 1.3 68.7 + - - +
5B PRO* 3.3 4.3 - - + -
6B GLU* 2.8 28.0 + - - +
7B LEU* 3.2 9.4 + - - +
54B LYS* 4.1 5.4 - - - +
173B GLY 4.0 4.3 - - - +
175B GLY* 1.9 53.5 + - - +
176B ASN 3.2 2.9 - - - -
177B TYR* 2.4 46.9 + - + -
178B LEU* 3.3 7.1 + - + -
297E CTG 3.0 12.8 - - - +
298E G 2.9 18.8 - - - +
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Residues in contact with GLY 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLU* 1.3 73.2 - - - +
5B PRO* 1.3 64.3 - - - +
7B LEU* 3.2 4.9 + - - +
8B HIS* 3.1 21.0 + - - +
53B GLY* 4.0 12.6 - - - +
54B LYS* 4.3 0.4 - - - +
137B VAL* 5.9 1.8 - - - -
138B LEU* 3.9 11.1 - - - +
173B GLY* 2.8 35.8 + - - -
233B PRO* 5.8 0.9 - - - -
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Residues in contact with PRO 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLU 3.4 0.4 - - - -
4B GLY* 1.3 87.1 - - - +
6B GLU* 1.3 76.5 + - - +
8B HIS* 3.2 1.7 + - - +
9B LEU* 2.8 35.8 + - + +
138B LEU* 4.1 2.5 - - + -
177B TYR* 3.7 12.8 - - - +
178B LEU* 3.8 13.7 - - + -
233B PRO* 3.7 31.2 - - + +
236B VAL* 3.8 15.3 - - + -
237B VAL* 3.7 22.8 - - + +
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Residues in contact with GLU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLY 3.6 10.3 - - - +
3B GLU* 2.8 28.2 + - - +
5B PRO* 1.3 79.9 - - - +
7B LEU* 1.3 69.3 + - + +
9B LEU* 4.1 6.5 - - - +
10B ALA* 3.0 25.2 + - - +
79B PHE* 4.6 5.0 - - + -
177B TYR* 2.8 29.5 + - - -
236B VAL* 4.0 0.9 - - - +
242B ARG* 3.7 38.8 + - - +
244B TYR* 4.7 5.6 - - + -
297E CTG 3.4 19.9 - - - +
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Residues in contact with LEU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLY 3.7 20.9 - - - +
3B GLU 3.2 16.5 + - - +
4B GLY 3.2 1.5 + - - +
6B GLU* 1.3 77.6 - - + +
8B HIS* 1.3 63.4 + - - +
10B ALA* 3.3 5.5 + - - +
11B SER* 3.1 18.4 + - - -
51B ALA* 3.8 10.4 - - + +
53B GLY 3.7 15.5 - - - +
54B LYS* 3.7 31.9 - - + +
55B GLU* 3.9 20.9 - - - +
56B LEU* 3.8 6.8 - - + +
77B PHE 4.4 0.7 - - - +
79B PHE* 3.7 48.7 - - + -
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Residues in contact with HIS 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLN* 6.3 1.6 - - - -
4B GLY 3.1 12.3 + - - +
5B PRO* 3.4 7.9 - - + +
6B GLU 3.1 0.4 - - - -
7B LEU* 1.3 78.3 - - - +
9B LEU* 1.3 62.1 + - - +
11B SER* 3.2 6.0 + - - -
12B GLN* 3.1 50.5 + - + +
51B ALA* 3.9 14.4 - - + +
138B LEU* 3.8 23.1 - - + +
139B GLN* 3.8 37.8 + - + +
237B VAL* 3.9 19.2 - - + +
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PRO* 2.8 30.8 + - + +
6B GLU* 4.1 4.9 - - - +
8B HIS* 1.3 71.2 - - - +
10B ALA* 1.3 58.4 + - - +
12B GLN* 3.3 18.1 + - - +
13B PHE* 2.9 29.6 + - - +
236B VAL 4.4 1.8 - - - +
237B VAL* 3.5 35.0 - - + +
240B GLY* 2.8 39.0 - - - +
241B GLY* 3.8 13.6 - - - +
242B ARG* 4.0 22.4 - - - -
244B TYR* 4.4 10.9 - - + +
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Residues in contact with ALA 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU 3.0 19.5 + - - +
7B LEU 3.4 5.6 - - - +
8B HIS 3.2 0.2 - - - -
9B LEU* 1.3 77.7 - - - +
11B SER* 1.3 56.9 + - - +
13B PHE* 3.2 5.0 - - - +
14B VAL* 3.1 32.7 + - - +
56B LEU* 3.9 5.2 - - + -
79B PHE* 3.8 23.1 - - + -
85B PHE* 4.7 3.1 - - + -
244B TYR* 3.5 30.9 - - + +
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Residues in contact with SER 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU 3.1 12.3 + - - -
8B HIS* 3.2 11.0 + - - -
10B ALA* 1.3 71.7 - - - +
12B GLN* 1.3 67.5 + - - +
13B PHE 3.1 0.9 - - - -
14B VAL 3.3 0.7 + - - -
15B ASN* 3.0 30.7 + - - -
49B ALA* 3.1 14.8 + - - +
50B SER* 2.9 37.7 + - - -
51B ALA* 3.9 13.2 - - - -
56B LEU* 3.7 5.8 - - - +
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Residues in contact with GLN 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B HIS* 3.1 42.0 + - + +
9B LEU* 3.5 18.5 - - - +
11B SER* 1.3 80.0 - - - +
13B PHE* 1.3 64.9 + - - +
15B ASN* 3.3 7.2 + - - +
16B GLU* 2.8 45.9 + - - +
237B VAL* 4.2 9.7 - - - +
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Residues in contact with PHE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU 2.9 13.9 + - - +
10B ALA 3.2 8.7 - - - +
12B GLN* 1.3 78.3 - - - +
14B VAL* 1.3 68.2 + - + +
16B GLU* 3.7 9.9 - - + +
17B ALA* 2.8 44.1 + - + +
85B PHE* 3.6 26.7 - - + -
86B GLN* 4.3 1.8 - - - -
87B LEU* 4.0 30.5 - - + -
112B LEU* 4.8 4.9 - - + -
244B TYR* 3.3 57.0 - + + -
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Residues in contact with VAL 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ALA 3.1 18.2 + - - +
11B SER* 3.3 3.8 + - - +
13B PHE* 1.3 78.9 - - + +
15B ASN* 1.3 64.5 + - - +
17B ALA* 5.0 0.9 - - - -
18B CYS* 2.9 38.1 + - + +
47B ILE* 4.2 7.6 - - + +
48B SER 4.8 1.8 - - - -
49B ALA* 4.0 10.8 - - + -
56B LEU* 5.5 0.4 - - + -
58B LEU* 3.8 25.6 - - + -
85B PHE* 4.1 33.0 - - + -
112B LEU* 4.0 22.4 - - + -
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Residues in contact with ASN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B SER* 3.0 24.6 + - - +
12B GLN* 3.8 6.1 - - - +
14B VAL* 1.3 75.6 - - - +
16B GLU* 1.3 62.6 + - + +
18B CYS* 4.0 1.3 - - - -
19B ARG* 3.2 29.0 + - - +
47B ILE 5.4 0.4 - - - -
48B SER* 3.3 15.4 - - - +
49B ALA 2.6 46.6 + - - +
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Residues in contact with GLU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLN* 2.8 43.3 + - - +
13B PHE* 3.7 9.1 - - + +
15B ASN* 1.3 74.0 - - + +
17B ALA* 1.3 67.7 + - + +
18B CYS 3.0 1.2 + - - -
19B ARG* 3.3 43.4 + - - +
20B ALA 5.0 0.2 + - - -
244B TYR 5.6 1.7 - - - +
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Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PHE* 2.8 41.3 + - + +
14B VAL* 4.5 1.6 - - - +
16B GLU* 1.3 75.6 - - - +
18B CYS* 1.3 63.2 + - - +
19B ARG 3.4 0.2 - - - -
20B ALA 4.9 0.9 + - - -
21B LEU* 3.2 21.7 - - - +
87B LEU* 4.0 21.6 - - + +
112B LEU* 6.2 0.4 - - + -
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Residues in contact with CYS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 2.9 24.4 + - - +
15B ASN 4.0 0.7 - - - +
17B ALA* 1.3 85.8 - - - +
19B ARG* 1.3 68.2 + - - +
20B ALA 3.3 2.7 - - - -
21B LEU* 3.1 23.4 + - - +
23B PHE* 3.8 30.6 - - + -
46B ARG* 5.8 1.6 - - - +
47B ILE* 3.8 23.8 + - - +
87B LEU* 5.1 2.2 - - - -
112B LEU* 4.0 28.5 - - - -
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Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASN 3.2 13.6 + - - +
16B GLU* 3.3 46.8 + - - +
17B ALA 3.4 0.2 - - - -
18B CYS* 1.3 81.0 - - - +
20B ALA* 1.3 61.9 + - + +
21B LEU 3.5 2.9 + - - +
46B ARG* 4.3 14.2 + - - -
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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