Contacts of the strand formed by residues 125 - 134 (chain A) in PDB entry 3NJ0
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 LYS 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.8 15.6 - - + -
111A SER* 5.8 1.3 - - - +
112A PHE 3.4 12.8 - - - +
113A ARG* 3.8 41.0 - - + +
123A ASN* 3.7 24.4 + - - +
124A TYR* 1.3 77.5 - - - +
126A SER* 1.3 61.4 + - - +
149A TYR* 3.2 6.4 - - - +
150A THR* 3.0 61.2 + - + +
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 4.6 0.2 - - - -
110A LEU 4.0 0.6 + - - +
111A SER* 3.2 8.5 + - - -
112A PHE* 2.9 55.4 + - - -
124A TYR* 3.6 16.6 - - - -
125A LYS* 1.3 76.6 - - - +
127A VAL* 1.3 64.5 + - - +
128A THR* 3.9 4.4 + - - -
147A GLU* 2.7 30.7 + - - +
148A SER 3.3 6.5 - - - -
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Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.4 27.1 - - + +
26A HIS* 3.3 15.5 - - + -
28A PHE* 4.0 21.1 - - + -
102A PHE* 6.2 0.2 - - + -
109A VAL* 3.8 25.6 - - + -
110A LEU 3.5 4.3 - - - +
111A SER* 3.8 14.8 - - - +
126A SER* 1.3 78.4 - - - +
128A THR* 1.3 63.1 + - - +
147A GLU* 3.3 1.6 - - - -
148A SER* 2.9 41.7 + - - +
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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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26A HIS* 4.0 1.3 - - - -
51A TRP* 5.0 0.7 - - - -
54A ILE* 3.9 32.3 - - + -
63A TYR* 5.0 5.4 + - - +
108A ARG 3.8 0.7 - - - +
109A VAL* 3.2 4.3 - - - +
110A LEU* 2.9 42.0 + - - +
112A PHE* 5.7 1.9 - - - -
126A SER* 3.9 3.8 + - - -
127A VAL* 1.3 75.7 - - - +
129A SER* 1.3 67.5 + - - +
130A VAL* 4.7 0.4 - - + -
145A VAL* 3.7 22.4 - - + -
146A LEU 3.2 10.1 - - - +
147A GLU* 3.6 24.2 - - + +
174A LEU* 5.4 1.6 - - + -
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Residues in contact with SER 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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21A VAL* 3.6 13.4 - - - +
26A HIS* 2.8 27.4 + - - -
107A HIS 4.9 0.9 - - - -
108A ARG 3.2 7.9 - - - -
109A VAL* 3.9 17.0 - - - -
128A THR* 1.3 73.5 - - - +
130A VAL* 1.3 64.6 + - - +
131A ASN* 3.1 18.9 + - - -
145A VAL* 3.3 7.1 - - - +
146A LEU* 2.8 35.4 + - - +
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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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47A ALA* 3.8 20.2 - - + +
50A VAL* 3.9 15.5 - - + -
51A TRP* 4.0 15.9 - - + +
54A ILE* 3.4 32.8 - - + -
107A HIS 3.9 4.0 - - - +
108A ARG* 2.9 38.9 + - + +
128A THR* 4.7 0.4 - - + -
129A SER* 1.3 79.2 - - - +
131A ASN* 1.3 64.9 - - - +
132A GLU 4.3 0.7 + - - -
143A THR* 3.5 25.1 - - + -
144A VAL 4.0 2.0 - - - -
145A VAL* 4.3 3.4 - - + -
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Residues in contact with ASN 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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18A LEU* 3.5 30.7 - - + +
21A VAL* 3.6 23.7 - - - +
47A ALA* 4.9 0.4 - - - -
107A HIS 4.9 3.5 - - - +
129A SER* 3.1 30.2 + - - -
130A VAL* 1.3 78.7 - - - +
132A GLU* 1.3 60.1 + - - +
133A PHE* 3.6 7.6 - - + -
143A THR* 3.3 4.9 - - - -
144A VAL 2.7 48.0 + - - +
146A LEU* 4.0 7.1 - - - +
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Residues in contact with GLU 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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17A THR* 6.0 0.7 - - - +
46A PRO* 3.4 10.7 - - - +
47A ALA* 2.7 42.2 + - + +
48A SER 4.3 1.4 + - - -
108A ARG* 4.9 8.1 + - - +
130A VAL 4.3 0.8 + - - -
131A ASN* 1.3 73.6 - - - +
133A PHE* 1.3 78.0 + - - +
141A VAL* 4.2 20.8 - - + +
142A TYR 3.4 12.3 - - - +
143A THR* 4.4 0.4 - - - +
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Residues in contact with PHE 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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13A GLU* 5.4 5.2 - - + -
14A GLU* 3.9 17.9 - - + -
17A THR* 3.8 33.0 - - + -
18A LEU* 3.8 28.3 - - + -
131A ASN* 3.6 23.1 - - + -
132A GLU* 1.3 82.4 - - - +
134A LEU* 1.3 62.1 + - - +
141A VAL* 3.3 10.5 - - - +
142A TYR* 2.8 61.5 + + + +
144A VAL* 3.7 30.7 - - + -
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Residues in contact with LEU 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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13A GLU* 5.5 2.6 - - - +
133A PHE* 1.3 76.5 - - - +
135A ASN* 1.3 63.8 + - - +
136A GLN* 3.4 45.9 + - + +
139A GLY* 3.4 34.8 - - - +
140A LYS 3.6 5.4 - - - +
141A VAL* 4.2 9.9 - - + -
142A TYR* 4.3 6.2 + - - -
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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