Contacts of the strand formed by residues 122 - 127 (chain B) in PDB entry 1PJT
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 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A VAL* 3.9 7.9 - - + -
127A SER 3.0 23.1 - - - +
128A ALA* 4.3 4.5 - - + +
135A LEU* 4.1 28.5 - - + -
136A ALA* 5.1 2.9 - - - -
139A LEU* 3.6 34.3 - - + -
119B ARG* 2.7 63.5 + - + +
120B SER 3.2 0.3 + - - -
121B PRO* 1.3 73.4 - - - +
123B MET* 1.3 60.8 + - - +
124B VAL* 3.9 17.3 - - + -
147B LEU* 4.4 7.0 - - + -
151B LEU* 4.5 7.4 - - + -
152B GLY* 5.1 2.0 - - - +
155B ALA* 4.9 3.8 - - + -
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Residues in contact with MET 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.4 34.1 - - + -
2A ASP* 4.4 2.7 - - - +
3A HIS* 3.2 43.5 - - - +
5A PRO* 3.9 13.2 - - + -
126A VAL* 3.3 5.0 - - - -
127A SER 2.9 30.6 + - - +
7B PHE* 3.5 18.6 - - + -
116B ILE* 4.0 13.2 - - + -
117B ILE 3.5 4.3 - - - +
118B ASP* 3.9 13.2 - - + +
120B SER* 4.0 5.8 - - - +
121B PRO 4.0 10.3 - - - +
122B LEU* 1.3 82.7 - - - +
124B VAL* 1.3 64.8 + - - +
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 5.5 0.4 - - - -
124A VAL* 3.8 21.5 - - + -
125A ALA 3.2 13.2 - - - +
126A VAL* 4.3 13.0 - - + -
139A LEU* 5.1 1.3 - - + -
143A LEU* 4.5 8.1 - - + -
7B PHE* 5.1 0.7 - - - -
116B ILE* 3.5 4.9 - - - +
117B ILE* 2.7 50.1 + - + +
122B LEU* 3.9 12.8 - - + -
123B MET* 1.3 79.4 - - - +
125B ALA* 1.3 58.7 + - - +
143B LEU* 4.2 14.4 - - + -
147B LEU* 3.7 29.4 - - + -
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Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 4.0 18.6 - - + -
7A PHE* 3.9 14.1 - - + -
123A MET 3.8 0.3 - - - +
124A VAL* 3.2 10.0 - - - +
125A ALA* 2.9 35.1 + - + +
7B PHE* 4.6 0.9 - - + -
114B PRO* 3.8 21.8 - - + -
115B SER 3.2 10.5 - - - +
124B VAL* 1.3 75.3 - - - +
126B VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 4.5 0.2 - - - -
122A LEU* 4.0 11.2 - - + -
123A MET 3.4 4.5 - - - +
124A VAL* 4.2 9.4 - - + -
114B PRO* 3.8 1.3 - - - +
115B SER* 2.9 45.2 + - - -
117B ILE* 4.1 9.9 - - + -
125B ALA* 1.3 80.5 - - - +
127B SER* 1.3 65.6 + - - +
136B ALA* 4.3 12.9 - - - +
139B LEU* 3.8 36.1 - - + -
140B ARG 4.7 2.2 - - - +
143B LEU* 3.7 30.1 - - + -
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Residues in contact with SER 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.5 29.9 - - - -
121A PRO 3.5 1.9 - - - +
122A LEU* 3.0 6.1 - - - +
123A MET* 2.6 42.6 + - - +
112B ILE* 3.6 24.1 - - - +
113B MET 4.6 0.5 + - - -
114B PRO* 4.2 8.6 - - - +
126B VAL* 1.3 78.8 + - - +
128B ALA* 1.3 59.0 + - - +
129B GLY 3.5 6.3 + - - -
130B GLY 4.9 1.0 + - - -
136B ALA* 5.0 4.3 - - - -
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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
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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