Contacts of the strand formed by residues 120 - 125 (chain A) in PDB entry 2PWY
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 LEU 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A MET 3.0 7.2 + - - +
96A ARG* 3.4 47.7 - - + +
97A VAL* 2.8 31.2 + - - +
115A VAL* 3.6 2.9 - - - +
119A GLY* 1.3 76.3 - - - +
121A VAL* 1.3 81.7 + - - +
122A GLU* 3.5 22.9 - - + +
146A ASN* 3.5 12.8 - - - +
147A VAL 4.8 0.2 - - - -
148A ARG* 4.0 35.4 - - + +
164A TYR* 4.8 0.2 - - + -
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A VAL* 3.5 14.4 - - + +
99A GLU* 4.1 22.2 - - + +
108A THR* 4.2 12.8 - - + -
111A LEU* 3.7 23.1 - - + +
112A ALA* 3.6 39.0 - - + +
115A VAL* 3.9 3.6 - - + -
120A LEU* 1.3 76.4 - - - +
122A GLU* 1.3 59.4 - - - +
123A SER* 3.6 6.1 + - - -
146A ASN 2.9 12.7 + - - +
147A VAL* 3.5 7.9 - - + +
148A ARG 2.9 28.9 + - - +
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ARG* 4.1 2.9 + - - -
97A VAL 2.8 9.3 + - - +
98A LEU* 3.5 9.2 - - + +
99A GLU 2.9 23.9 + - - +
120A LEU* 3.5 13.0 - - + +
121A VAL* 1.3 70.0 - - - +
123A SER* 1.3 58.8 + - - +
124A TYR* 3.8 15.5 - - + +
148A ARG* 3.3 37.9 + - - +
150A HIS* 2.8 32.9 - - + -
159A LEU* 5.4 0.2 - - - -
164A TYR* 2.7 44.3 + - + +
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A GLU* 2.7 34.4 + - - -
102A THR* 2.7 30.9 + - - +
108A THR* 4.8 0.2 - - - -
121A VAL* 3.6 8.7 + - - -
122A GLU* 1.3 73.0 - - - +
124A TYR* 1.3 62.6 + - - +
147A VAL* 4.5 10.5 - - - -
148A ARG 2.9 12.3 + - - +
149A PHE* 3.5 3.2 - - - -
150A HIS* 2.8 30.0 + - - +
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Residues in contact with TYR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 3.8 21.1 - - + -
99A GLU 2.8 14.0 + - - +
100A ALA* 3.6 11.6 - - + +
101A GLY* 3.2 10.6 - - - -
102A THR* 2.9 20.3 + - - -
122A GLU* 3.8 12.9 - - + +
123A SER* 1.3 75.8 + - - +
125A GLU* 1.3 60.9 + - - +
150A HIS* 3.4 51.8 + + + -
152A GLY* 4.0 17.9 - - - +
153A LYS 4.5 2.5 - - - -
154A LEU* 3.8 25.4 - - + +
157A ALA* 3.4 27.4 - - + +
158A GLU 4.2 4.7 + - - -
159A LEU* 3.4 17.9 - - + +
501A SAH 3.9 1.9 - - + -
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A THR* 3.4 17.4 + - - +
103A GLY 2.8 20.7 + - - +
124A TYR* 1.3 75.0 - - - +
126A ALA* 1.3 63.0 + - - +
127A ARG* 2.8 35.8 + - - +
130A HIS* 3.8 6.7 - - + -
131A LEU* 3.7 25.8 - - + +
150A HIS 2.9 7.3 + - - -
151A LEU* 3.4 10.4 - - - +
152A GLY 2.9 21.2 + - - -
501A SAH 2.6 52.7 + - - -
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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