Contacts of the strand formed by residues 142 - 147 (chain G) in PDB entry 3PHW
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 142 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45G ILE* 4.1 19.1 - - + -
48G LEU* 3.9 23.8 - - + +
49G THR* 3.8 18.2 - - + -
114G ILE* 3.8 27.8 - - + -
115G THR 2.9 8.1 + - - +
116G ILE* 3.7 24.6 - - + +
117G ILE 3.0 23.5 + - - +
140G THR 5.1 2.5 - - - +
141G ALA* 1.3 74.7 - - - +
143G ASN* 1.3 59.5 + - - +
144G LEU* 3.8 6.2 + - + -
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Residues in contact with ASN 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G PHE* 3.8 16.9 - - + -
48G LEU* 3.2 13.2 - - - +
117G ILE* 3.6 14.3 - - - +
119G TRP* 2.9 28.5 + - + +
138G VAL* 3.3 33.4 + - - +
141G ALA* 3.5 10.6 + - - -
142G VAL* 1.3 73.1 - - - +
144G LEU* 1.3 60.2 - - - +
155G LEU* 2.9 48.0 + - + +
157G ILE* 4.5 5.1 - - - +
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Residues in contact with LEU 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G PHE* 3.6 27.1 - - + -
44G SER* 4.0 26.0 - - - -
45G ILE* 3.6 34.3 - - + -
48G LEU* 4.2 12.6 - - + -
116G ILE* 4.4 11.4 - - + -
117G ILE 2.9 12.8 + - - +
118G ILE* 4.3 12.1 - - + -
119G TRP* 2.7 36.3 + - - +
142G VAL* 4.2 7.0 - - + +
143G ASN* 1.3 80.8 - - - +
145G LEU* 1.3 56.4 + - - +
146G HIS 4.1 0.4 - - - -
152G PHE* 4.3 11.2 - - + -
153G ASP 3.5 4.5 - - - +
155G LEU* 3.7 4.4 - - - +
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Residues in contact with LEU 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G ILE* 3.5 25.4 - - + -
31G ILE* 4.0 28.9 - - + -
33G ARG* 4.3 15.0 - - - +
119G TRP 3.4 8.1 - - - +
121G VAL* 3.5 37.7 - - + -
125G ASP* 4.8 6.1 - - - +
144G LEU* 1.3 71.8 - - - +
146G HIS* 1.3 60.8 + - - +
147G SER* 3.8 10.0 + - - -
151G HIS 3.3 1.7 - - - +
152G PHE* 3.2 6.6 - - - -
153G ASP* 2.9 43.4 + - + +
155G LEU* 3.8 17.9 - - + +
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Residues in contact with HIS 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G ILE* 3.8 19.3 - - + +
119G TRP 2.7 14.3 + - - +
120G THR* 3.2 24.3 + - - +
121G VAL* 3.2 27.9 + - - +
144G LEU 4.1 0.8 - - - -
145G LEU* 1.3 72.1 - - - +
147G SER* 1.3 57.7 + - - +
149G GLN* 3.5 42.5 + - - -
150G THR 3.8 1.1 - - - -
151G HIS 3.2 11.2 + - - -
152G PHE* 3.7 18.8 - + + -
73H LEU* 3.8 25.4 - - + +
74H ARG 2.7 33.2 + - - -
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Residues in contact with SER 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B GLN* 4.6 3.8 + - - -
35B GLY 4.6 7.1 + - - -
37B PRO* 3.9 6.6 - - - +
33G ARG* 4.8 3.1 + - - -
121G VAL* 3.7 21.1 - - - -
123G ALA* 6.0 1.1 - - - -
125G ASP* 4.8 4.9 - - - -
145G LEU* 4.7 10.6 + - - -
146G HIS* 1.3 75.4 - - - +
148G GLY* 1.3 59.6 + - - +
149G GLN 2.8 11.1 + - - +
150G THR 3.0 11.6 + - - -
151G HIS* 2.8 38.0 + - - +
153G ASP* 4.5 5.9 + - - -
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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