Contacts of the strand formed by residues 173 - 179 (chain I) in PDB entry 3D29
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 ALA 173 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I CYS 3.1 14.8 - - - +
17I ASP* 4.2 1.6 - - + -
18I LEU* 3.5 11.1 - - - +
159I LEU* 3.6 22.9 - - + -
160I LEU* 4.7 0.9 - - + -
172I GLY* 1.3 78.1 - - - +
174I VAL* 1.3 61.0 + - - +
188I TYR* 3.3 9.9 - - - +
189I LEU* 3.0 44.6 + - + +
191I MET* 4.4 9.2 - - - -
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Residues in contact with VAL 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ALA* 3.2 5.5 - - - +
16I CYS* 2.9 57.3 + - - +
18I LEU* 4.2 8.7 - - + -
32I GLU* 4.5 8.3 - - + +
34I ILE* 4.9 0.2 - - + -
173I ALA* 1.3 75.4 - - - +
175I VAL* 1.3 66.6 + - - +
176I TYR* 4.3 14.4 - - + -
186I LYS* 3.3 43.3 - - + -
187I ARG 3.2 11.0 - - - +
188I TYR* 4.3 14.1 - - + -
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Residues in contact with VAL 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I ALA* 5.0 0.4 - - + -
14I ILE 3.8 3.4 - - - +
15I ALA* 3.7 15.0 - - + -
152I PHE* 3.8 24.5 - - + -
155I ILE* 3.8 25.6 - - + -
156I SER* 3.5 21.3 - - - +
159I LEU* 4.9 0.9 - - + -
174I VAL* 1.3 79.9 - - - +
176I TYR* 1.3 74.6 + - - +
177I ILE* 4.4 2.8 - - + +
185I VAL 3.7 1.0 - - - +
186I LYS* 3.4 4.0 - - - -
187I ARG* 2.8 33.8 + - - +
189I LEU* 3.5 22.9 - - + -
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Residues in contact with TYR 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219H VAL* 4.0 11.7 - - + -
12I VAL 3.9 0.5 - - - +
13I ALA* 3.1 28.9 - - - +
14I ILE* 2.9 30.1 + - + +
32I GLU* 4.1 3.3 + - - -
34I ILE* 3.5 44.2 + - + +
36I HIS* 5.6 4.3 - + - -
42I PHE* 3.9 20.6 - + - -
174I VAL* 4.3 14.8 - - + -
175I VAL* 1.3 77.8 - - - +
177I ILE* 1.3 62.0 + - - +
178I ILE* 3.9 9.4 - - + -
184I VAL* 4.2 11.2 - - + -
185I VAL 3.4 1.6 - - - -
186I LYS* 3.1 53.0 + - + +
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Residues in contact with ILE 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I CYS* 5.2 2.9 - - + -
12I VAL 4.0 2.0 - - - +
13I ALA* 3.8 15.5 - - + -
148I PRO* 3.9 33.2 - - + +
151I LEU* 4.6 2.9 - - + -
152I PHE* 3.6 37.9 - - + +
175I VAL* 4.4 3.4 - - + +
176I TYR* 1.3 78.4 - - - +
178I ILE* 1.3 63.8 + - - +
179I LYS* 4.8 10.5 - - + +
183I GLU 3.9 1.2 - - - +
184I VAL* 3.3 4.7 - - - +
185I VAL* 2.9 40.3 + - + +
187I ARG* 3.6 26.9 - - - +
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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
----------------------------------------------------------
11I CYS* 3.1 9.9 - - - +
12I VAL* 2.8 63.7 + - + +
14I ILE* 4.3 9.9 - - + -
40I HIS* 5.3 3.4 - - + +
42I PHE* 3.6 36.8 - - + -
102I ALA* 5.1 2.5 - - + +
103I GLY* 5.1 1.3 - - - -
104I ILE* 4.1 14.4 - - + +
176I TYR* 4.1 17.3 - - + +
177I ILE* 1.3 77.8 - - - +
179I LYS* 1.3 69.9 + - - +
183I GLU 4.0 1.8 - - - -
184I VAL* 3.9 27.1 - - + -
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Residues in contact with LYS 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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10I ASP 4.2 9.6 - - - +
11I CYS* 4.2 3.8 - - + -
104I ILE* 4.4 5.7 - - - +
148I PRO* 4.2 33.5 - - + +
149I GLU* 5.6 3.8 + - - -
177I ILE* 4.8 8.1 - - + +
178I ILE* 1.3 86.8 - - - +
181I LYS* 1.3 66.7 + - - +
182I ASP* 3.2 19.6 + - - +
183I GLU* 2.8 58.6 + - + +
184I VAL* 4.6 1.7 - - - +
185I VAL* 6.0 1.3 - - + -
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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