Contacts of the strand formed by residues 22 - 30 (chain Q) in PDB entry 5C3I
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 PHE 22 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13Q ASP* 4.6 2.0 - - - -
21Q PRO* 1.3 69.9 - - - +
23Q GLN* 1.3 60.8 + - - +
24Q PHE* 4.1 24.5 - + + -
42Q ILE* 5.0 1.1 - - + -
44Q TYR* 4.0 21.3 - + - -
57Q LEU* 3.5 31.9 - - + -
74Q PHE 3.3 1.7 - - - +
75Q GLN* 3.0 29.5 - - - +
76Q ALA* 2.7 23.3 + - + +
77Q ASP 4.0 3.6 - - - -
78Q ALA* 4.4 0.9 - - - -
79Q PRO* 3.9 15.9 - - + -
95Q VAL* 3.9 16.8 - - + -
137Q ARG* 3.4 42.2 - - - +
139Q ILE* 3.6 23.6 - - + -
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Residues in contact with GLN 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Q VAL* 3.9 2.6 - - - +
12Q LEU* 2.9 52.9 + - + +
13Q ASP* 3.9 28.6 + - - +
21Q PRO* 3.6 10.3 + - + +
22Q PHE* 1.3 78.3 - - - +
24Q PHE* 1.3 67.4 + - - +
73Q VAL* 4.4 6.8 - - + +
74Q PHE 3.6 2.9 - - - -
75Q GLN* 3.4 32.8 + - + +
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Residues in contact with PHE 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q VAL* 4.0 13.9 - - + -
10Q VAL 3.6 1.3 - - - -
11Q VAL* 4.0 31.0 - - + -
12Q LEU* 4.5 0.7 - - - -
22Q PHE* 4.1 25.1 - + + -
23Q GLN* 1.3 79.3 - - - +
25Q GLU* 1.3 60.7 + - - +
26Q ILE* 3.7 8.9 + - + -
42Q ILE* 3.6 36.8 - - + -
73Q VAL* 3.1 10.1 - - - +
74Q PHE* 2.9 36.9 + - + +
95Q VAL* 4.0 16.8 - - + -
97Q ILE* 3.5 38.6 - - + -
111Q TYR* 4.1 10.1 - + - -
139Q ILE* 4.9 4.5 - - + -
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Residues in contact with GLU 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Q ASN* 3.5 2.8 + - - +
9Q VAL* 3.5 4.2 - - - +
10Q VAL* 2.9 56.4 + - + +
12Q LEU* 3.7 25.5 - - + +
24Q PHE* 1.3 72.4 - - - +
26Q ILE* 1.3 62.2 + - - +
27Q THR* 3.7 5.7 + - - -
71Q MET* 4.0 27.9 - - + +
72Q PHE 4.0 2.2 - - - -
73Q VAL* 4.4 8.2 - - + +
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Residues in contact with ILE 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Q VAL* 4.5 4.7 - - + -
8Q ASN 3.5 6.1 - - - +
9Q VAL* 4.1 13.7 - - + -
24Q PHE* 4.4 12.6 - - + -
25Q GLU* 1.3 73.5 - - - +
27Q THR* 1.3 69.5 - - - +
28Q PHE* 4.4 1.1 - - + +
40Q TRP* 3.6 43.5 - - + -
70Q HIS 3.8 0.7 - - - +
71Q MET* 3.1 6.6 - - - +
72Q PHE* 3.0 67.2 + - + +
74Q PHE* 3.9 19.7 - - + -
97Q ILE* 4.0 15.0 - - + -
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Residues in contact with THR 27 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Q VAL* 3.7 2.3 - - - +
7Q ASN* 2.7 46.3 + - + +
8Q ASN* 2.9 33.3 + - + +
25Q GLU* 4.4 6.6 + - - -
26Q ILE* 1.3 73.3 - - - +
28Q PHE* 1.3 54.6 + - - +
69Q ARG* 4.6 14.8 - - + -
70Q HIS 3.4 10.5 - - - +
71Q MET* 3.8 17.1 - - + +
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Residues in contact with PHE 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q VAL* 4.1 16.8 - - + -
5Q GLN 3.4 10.8 - - - +
6Q VAL* 4.3 3.8 - - - -
7Q ASN* 4.1 3.1 - - - +
26Q ILE* 4.5 1.6 - - + -
27Q THR* 1.3 75.0 - - - +
29Q GLU* 1.3 64.5 + - - +
30Q CYS* 4.8 4.5 - - + -
38Q LEU* 3.9 20.0 - - + -
40Q TRP* 4.0 28.9 - + + -
62Q VAL* 4.3 16.6 - - + -
65Q VAL* 4.0 23.6 - - + -
68Q GLY 3.7 1.0 - - - +
69Q ARG* 3.7 1.6 - - - +
70Q HIS* 3.0 66.5 + + + -
72Q PHE* 4.0 29.4 - + - -
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Residues in contact with GLU 29 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q VAL* 3.3 6.8 - - - +
5Q GLN* 2.7 52.3 + - + +
7Q ASN* 3.4 21.9 + - - +
28Q PHE* 1.3 76.0 - - - +
30Q CYS* 1.3 63.7 + - - +
31Q ILE* 3.8 22.8 + - + +
68Q GLY* 3.4 5.4 - - - +
69Q ARG* 2.7 44.0 + - - +
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Residues in contact with CYS 30 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Q LYS 3.8 2.5 - - - -
4Q VAL* 3.9 20.9 - - - -
28Q PHE* 4.1 4.0 + - + -
29Q GLU* 1.3 73.3 - - - +
31Q ILE* 1.3 64.2 + - - +
32Q GLU 3.2 20.3 + - - -
34Q LEU* 4.0 11.2 - - - -
65Q VAL* 3.9 27.8 - - - -
66Q PRO 3.4 18.8 - - - +
67Q ALA* 3.3 4.7 - - - +
68Q GLY* 2.9 30.9 + - - +
70Q HIS* 4.3 5.8 - - + -
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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