Contacts of the strand formed by residues 173 - 179 (chain I) in PDB entry 5A0Q
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 ILE 173 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15I GLY* 5.4 0.4 - - - -
16I ALA 3.2 9.4 - - - +
17I ASP* 4.4 0.9 - - - +
155I VAL 4.7 0.7 - - - +
156I SER* 2.9 43.1 - - - +
159I ILE* 4.0 17.3 - - + -
160I ALA* 4.1 15.5 - - + +
163I ILE* 3.6 18.8 - - + -
171I SER 4.3 0.2 - - - -
172I ASN* 1.3 73.4 - - - +
174I ASP* 1.3 73.2 + - - +
175I LEU* 5.0 4.9 - - + -
189I TYR* 3.0 24.3 + - + +
190I THR* 3.1 40.6 + - + +
192I PRO* 4.3 5.4 - - + -
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Residues in contact with ASP 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I GLY* 3.3 3.3 - - - -
16I ALA* 2.4 46.3 + - + +
17I ASP 5.1 0.3 - - - +
18I THR* 3.1 23.6 - - - +
31I CYS 4.3 4.9 - - - +
32I SER* 4.8 0.2 - - - -
33I LYS 4.7 7.3 + - - -
34I ILE* 4.0 20.2 + - + +
173I ILE* 1.3 80.5 - - - +
175I LEU* 1.3 62.9 + - - +
185I PHE* 5.1 6.0 - - + -
186I LEU 4.0 5.8 - - - +
187I ARG* 2.7 44.1 + - - +
188I PRO* 4.4 0.2 - - - +
189I TYR* 4.3 0.6 + - - -
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Residues in contact with LEU 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I VAL* 3.4 34.8 - - + -
14I LEU 3.6 4.0 - - - +
15I GLY* 4.9 0.2 - - - -
152I LYS* 3.9 37.9 - - + +
155I VAL* 3.9 18.8 - - + -
156I SER* 4.3 6.1 - - - +
173I ILE* 5.0 2.2 - - + -
174I ASP* 1.3 78.2 - - - +
176I CYS* 1.3 59.9 + - - +
177I VAL* 3.7 22.2 - - + -
186I LEU* 3.1 43.0 + - + +
189I TYR* 3.4 27.6 - - + +
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Residues in contact with CYS 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I ILE 3.8 0.9 - - - +
14I LEU* 2.9 40.1 + - + +
34I ILE* 3.7 26.0 - - + +
42I TYR* 3.3 43.1 - - - -
175I LEU* 1.3 75.9 - - - +
177I VAL* 1.4 60.6 + - - +
178I ILE* 4.7 0.9 - - - +
184I ASP 3.2 18.2 - - - +
185I PHE* 4.0 18.8 - - + -
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Residues in contact with VAL 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I TYR* 3.0 31.9 - - + +
12I ILE 3.9 2.9 - - - -
13I VAL* 4.4 3.4 - - + +
148I GLU* 4.9 2.2 - - - +
152I LYS* 3.6 34.3 - - - +
175I LEU* 3.7 17.0 - - + -
176I CYS* 1.4 74.6 - - - +
178I ILE* 1.3 68.9 + - - +
179I SER* 4.2 6.1 - - - +
182I LYS 5.1 0.2 - - - +
183I LEU* 4.0 3.3 - - - +
184I ASP* 3.3 52.5 + - + +
186I LEU* 5.0 2.5 - - + -
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Residues in contact with ILE 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I TYR* 3.6 2.1 + - - -
11I GLY* 3.3 5.5 - - - -
12I ILE* 2.9 49.5 + - + +
14I LEU* 5.3 4.3 - - + -
40I ASN 3.3 22.2 - - - +
41I ILE* 4.9 0.4 - - - -
42I TYR* 3.3 39.7 - - + -
101I GLY 4.6 10.3 - - - +
102I GLY* 4.0 9.6 - - - -
103I VAL* 3.4 28.5 - - + +
176I CYS 4.7 2.9 - - - +
177I VAL* 1.3 76.6 - - - +
179I SER* 1.3 63.6 + - - +
182I LYS 4.9 0.2 - - - -
183I LEU* 3.8 12.1 - - + -
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Residues in contact with SER 179 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I TYR* 3.6 13.4 + - - -
10I ASP* 3.4 21.3 - - - -
103I VAL* 4.6 6.3 - - - -
148I GLU* 3.8 9.7 + - - -
177I VAL* 4.4 3.6 - - - +
178I ILE* 1.3 77.9 - - - +
180I LYS* 1.4 61.2 + - - +
181I ASN* 3.7 13.8 - - - +
182I LYS* 2.8 41.9 + - - +
183I LEU* 3.3 14.9 - - - +
184I ASP* 5.4 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
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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