Contacts of the strand formed by residues 127 - 134 (chain A) in PDB entry 5J63
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 GLU 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A LEU* 4.0 13.4 - - + +
120A VAL* 4.9 0.5 - - - +
125A GLU* 3.5 19.8 + - - +
126A THR* 1.3 85.6 + - - +
128A THR* 1.3 65.4 + - - +
149A ARG* 3.2 45.2 + - - +
150A ILE 3.5 13.4 - - - +
151A ALA* 4.2 5.6 - - + +
152A ILE* 3.8 6.3 - - - +
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Residues in contact with THR 128 (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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105A GLY 3.7 16.5 + - - -
106A SER* 3.8 6.2 - - - -
107A LEU* 3.6 21.5 + - - +
120A VAL* 4.1 21.8 - - + +
127A GLU* 1.3 76.0 - - - +
129A GLY* 1.3 64.5 + - - +
149A ARG* 3.5 5.9 - - - +
150A ILE* 2.8 32.0 + - + +
152A ILE* 3.8 22.9 - - + -
161A LEU* 3.9 18.6 - - + -
165A LEU* 4.1 12.5 - - + +
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Residues in contact with GLY 129 (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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105A GLY 3.0 7.4 - - - -
106A SER 2.9 22.9 + - - -
107A LEU* 3.8 11.4 - - - +
128A THR* 1.3 85.9 + - - +
130A VAL* 1.3 63.9 + - - -
148A LEU 3.0 13.2 - - - -
149A ARG* 4.2 0.4 - - - -
150A ILE* 4.3 8.5 - - - -
165A LEU* 3.3 10.1 - - - +
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Residues in contact with VAL 130 (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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11A MET* 4.2 11.9 - - + -
103A LEU* 4.5 4.3 - - + -
104A HIS 3.4 5.6 - - - +
105A GLY* 4.3 4.0 - - - +
106A SER 4.0 0.4 + - - -
107A LEU* 5.0 0.4 - - - +
129A GLY* 1.3 79.9 - - - +
131A THR* 1.3 61.4 + - - +
147A GLN* 3.2 6.6 - - - +
148A LEU* 2.8 46.5 + - + +
165A LEU* 3.5 33.7 - - + +
168A ALA* 3.8 27.4 - - + -
169A ALA* 3.8 5.6 - - + +
172A LEU* 3.3 21.8 - - + +
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Residues in contact with THR 131 (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 ASN 3.7 0.9 - - - +
103A LEU* 3.3 3.6 - - - +
104A HIS* 2.8 33.3 + - - +
106A SER 2.8 18.6 + - - -
108A LEU* 3.4 27.8 + - + -
130A VAL* 1.3 72.6 - - - +
132A LEU* 1.3 72.3 + - - +
133A HIS* 4.2 1.3 - - + -
144A ILE* 3.9 24.0 - - + -
146A ALA 3.4 12.3 - - - +
147A GLN* 2.6 26.7 + - - +
172A LEU* 4.1 3.1 - - - -
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Residues in contact with LEU 132 (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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80A PHE* 4.4 12.3 - - + -
82A PHE* 5.1 0.4 - - + -
101A PHE* 4.0 17.7 - - + -
102A ASN 3.2 23.8 - - - +
103A LEU* 4.1 11.7 - - + +
131A THR* 1.3 74.8 - - - +
133A HIS* 1.3 63.4 + - - +
145A VAL* 3.1 28.9 + - + -
146A ALA 3.0 12.4 + - - +
172A LEU* 3.5 21.1 - - + +
173A LEU* 4.6 14.1 - - + -
176A THR* 3.3 34.3 - - + -
180A ILE* 3.8 16.4 - - + -
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Residues in contact with HIS 133 (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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101A PHE* 3.1 11.8 - - - +
102A ASN* 2.9 69.9 + - + -
104A HIS* 4.4 2.6 - - + +
108A LEU* 3.2 32.0 - - + +
131A THR* 4.2 6.5 - - + -
132A LEU* 1.3 77.2 - - - +
134A ARG* 1.3 86.1 + - - +
135A MET* 4.6 3.6 - - - -
136A VAL 5.6 0.2 - - - -
140A ASP* 3.7 29.0 - - - -
141A ALA 4.1 1.3 - - - -
142A GLY 3.7 13.8 + - - +
143A ALA 3.2 16.2 - - - +
144A ILE* 4.0 4.9 - - + -
145A VAL* 4.2 2.9 - - - -
190A GLN* 4.3 0.2 - - - -
402A FNX 4.7 2.0 - - - -
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Residues in contact with ARG 134 (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 ALA 3.1 28.3 + - - -
99A GLY* 3.3 16.8 - - - -
100A ALA 3.4 7.6 - - - +
101A PHE* 3.5 24.9 - - + -
133A HIS* 1.3 93.6 + - - +
135A MET* 1.3 57.9 + - - +
136A VAL* 4.8 8.7 - - + -
142A GLY* 3.2 15.4 + - - -
143A ALA* 2.9 28.7 + - + +
145A VAL* 4.2 2.8 - - + +
185A ILE* 4.7 8.9 - - - +
187A GLU* 3.2 40.1 + - - +
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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