Contacts of the strand formed by residues 13 - 18 (chain I) in PDB entry 3IT8
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 VAL 13 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55H LEU* 3.6 17.0 - - + -
123H VAL* 4.0 20.4 - - + -
8I PRO* 5.3 1.6 - - + -
11I LYS 3.5 10.5 - - - +
12I PRO* 1.3 75.2 - - - +
14I ALA* 1.3 79.0 + - - +
36I LEU* 4.1 18.2 - - + -
38I ALA* 3.0 39.0 + - + -
39I ASN* 4.4 7.4 - - - +
41I VAL* 3.2 9.3 - - - +
154I ILE* 3.3 14.8 - - - +
155I ILE* 3.5 22.7 - - + -
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Residues in contact with ALA 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H VAL* 5.6 0.3 - - - +
13I VAL* 1.3 85.7 - - - +
15I HIS* 1.3 62.1 + - - +
16I VAL* 4.0 0.9 - - + -
36I LEU* 3.2 15.9 - - - +
37I LEU* 4.0 7.4 - - + -
41I VAL* 3.6 23.8 - - + -
48I LEU* 4.2 13.0 - - + -
59I TYR* 4.1 2.3 + - - -
153I GLY* 2.9 4.1 - - - -
154I ILE* 2.8 37.5 + - + +
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Residues in contact with HIS 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H LEU 4.9 2.2 + - - -
94H LEU* 4.5 0.2 - - + -
122H GLY* 4.3 1.6 - - - -
123H VAL* 3.7 17.6 + - + +
124H PHE* 3.7 25.8 - + - -
14I ALA* 1.3 73.9 - - - +
16I VAL* 1.3 60.5 + - - +
17I VAL* 5.5 4.3 - - + +
34I ASN 3.7 19.5 - - - +
35I ALA* 3.3 12.5 - - + +
36I LEU* 2.8 40.5 + - + +
59I TYR* 2.6 26.6 + + - +
151I TYR* 3.4 48.8 - + + +
152I PHE 3.5 3.5 + - - -
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Residues in contact with VAL 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I HIS* 1.3 78.6 - - - +
17I VAL* 1.3 61.5 + - - +
28I TRP* 3.6 31.1 - - + -
29I LEU 3.3 13.9 - - - +
30I ASN* 4.2 6.7 - - + -
36I LEU 4.0 11.0 - - - +
37I LEU* 4.8 2.7 - - + -
43I LEU* 4.0 19.7 - - + -
48I LEU* 4.1 19.3 - - + -
151I TYR* 3.3 6.2 - - - +
152I PHE* 2.7 59.7 + - + +
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Residues in contact with VAL 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I HIS* 4.2 4.7 + - + +
16I VAL* 1.3 76.1 - - - +
18I ALA* 1.3 67.8 + - - +
28I TRP* 3.4 6.8 - - - -
29I LEU* 2.8 52.3 + - + +
32I ARG* 4.3 24.0 - - + +
35I ALA* 5.0 7.4 - - + +
147I SER 3.6 21.3 - - - +
148I GLY* 5.3 1.6 - - - -
150I VAL 2.9 23.1 - - - +
151I TYR* 4.7 4.7 - - + -
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Residues in contact with ALA 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I VAL* 1.3 87.1 - - + +
19I ASN* 1.3 59.3 + - - +
20I PRO* 3.3 15.6 - - - +
26I LEU* 3.7 14.8 - - + -
27I GLN 3.5 6.3 - - - +
28I TRP* 3.7 3.9 - - - -
29I LEU* 3.3 3.0 - - - +
32I ARG* 5.2 0.2 + - - -
144I PHE* 4.1 20.0 - - + +
150I VAL* 3.3 37.3 + - + -
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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
------------------------------------------------------------
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