Contacts of the strand formed by residues 141 - 152 (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 VAL 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A HIS* 4.6 4.3 + - - +
45A ALA* 4.5 7.1 + - - -
46A PRO* 3.9 38.4 - - + -
132A GLU* 4.2 18.2 - - - +
133A PHE 3.3 13.5 - - - +
134A LEU* 4.2 13.2 - - + -
139A GLY 4.7 3.4 - - - +
140A LYS* 1.3 81.2 - - - +
142A TYR* 1.3 64.3 + - - +
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Residues in contact with TYR 142 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLU* 2.6 38.0 + - - +
42A ARG* 3.4 29.6 - - + -
43A ILE 3.5 12.3 - - - +
44A HIS* 3.7 21.8 - + - +
45A ALA 3.7 5.8 - - - +
132A GLU* 3.4 6.4 - - - +
133A PHE* 2.8 60.4 + + + +
134A LEU 4.3 2.6 + - - -
135A ASN* 4.3 37.2 - - + -
141A VAL* 1.3 77.6 - - - +
143A THR* 1.3 65.4 + - - +
144A VAL* 3.9 8.7 - - + -
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Residues in contact with THR 143 (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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42A ARG* 3.4 5.0 - - - +
43A ILE* 2.7 40.3 + - + -
45A ALA 2.8 20.7 + - - -
46A PRO 3.5 0.5 + - - -
47A ALA* 3.2 22.2 + - - +
50A VAL* 4.1 9.4 - - + -
130A VAL* 3.5 30.5 - - + -
131A ASN 3.3 8.9 + - - +
142A TYR* 1.3 75.4 + - - +
144A VAL* 1.3 74.1 + - - +
145A VAL* 3.9 10.8 - - + -
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Residues in contact with VAL 144 (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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10A LEU* 3.6 26.9 - - + -
14A GLU* 4.2 13.7 - - - +
18A LEU* 3.9 13.0 - - + -
41A GLN 3.3 10.3 - - - +
42A ARG* 4.3 7.9 - - + -
131A ASN* 2.7 40.3 + - - -
133A PHE* 3.7 29.2 - - + -
142A TYR* 3.9 13.7 - - + -
143A THR* 1.3 80.2 - - - +
145A VAL* 1.3 68.0 + - - +
146A LEU* 4.1 6.1 - - + -
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Residues in contact with VAL 145 (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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39A ILE 3.9 0.3 - - - +
40A THR* 3.4 4.7 - - - -
41A GLN* 2.8 41.0 + - + +
43A ILE* 3.7 26.9 - - + -
50A VAL* 3.8 20.2 - - + -
54A ILE* 4.5 1.3 - - + -
128A THR* 3.7 22.9 - - + -
129A SER 3.3 9.6 - - - +
130A VAL* 4.3 4.3 - - + -
143A THR* 3.9 7.2 - - + -
144A VAL* 1.3 75.9 - - - +
146A LEU* 1.3 65.4 + - - +
174A LEU* 3.9 21.5 - - + +
177A LEU* 4.0 7.2 - - + -
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Residues in contact with LEU 146 (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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10A LEU* 4.7 2.5 - - + -
18A LEU* 4.3 20.0 - - + -
21A VAL* 4.4 4.5 - - + -
22A ILE* 3.6 31.0 - - + -
26A HIS* 3.4 14.4 - - + +
38A LEU* 4.1 11.7 - - + -
39A ILE 3.5 2.0 - - - +
40A THR* 3.4 31.6 - - + -
128A THR* 3.2 5.5 - - - +
129A SER* 2.8 48.4 + - - +
131A ASN* 4.0 13.0 - - - +
144A VAL* 4.1 11.4 - - + -
145A VAL* 1.3 77.2 - - - +
147A GLU* 1.3 60.6 + - - +
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Residues in contact with GLU 147 (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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37A SER 4.1 0.2 - - - +
38A LEU* 3.7 2.3 - - - -
39A ILE* 2.8 41.4 + - - +
63A TYR* 5.1 9.1 + - - -
64A LYS* 5.5 3.4 + - - -
112A PHE* 4.7 5.2 - - - -
124A TYR* 3.7 11.3 + - - +
126A SER* 2.7 31.4 + - - +
127A VAL 3.3 2.7 - - - +
128A THR* 3.6 14.5 + - - +
145A VAL 4.2 0.2 - - - -
146A LEU* 1.3 75.4 - - - +
148A SER* 1.3 65.6 + - - +
149A TYR* 5.0 1.5 - - + -
170A VAL* 3.7 31.6 - - + +
173A ASN* 5.7 1.9 - - - +
174A LEU* 3.7 24.7 - - + +
300A PYV 4.7 4.2 + - - -
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Residues in contact with SER 148 (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* 2.9 50.7 + - - +
28A PHE* 3.6 9.3 - - - -
37A SER 3.1 13.5 - - - -
38A LEU* 3.9 8.7 - - - -
126A SER* 3.3 5.9 + - - -
127A VAL* 2.9 33.4 + - - +
147A GLU* 1.3 76.8 - - - +
149A TYR* 1.3 62.9 + - - +
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Residues in contact with TYR 149 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.6 8.4 - - - -
35A CYS* 3.9 11.4 - - - -
36A THR* 3.1 25.8 - - - -
37A SER* 3.0 32.4 + - - +
39A ILE* 4.6 6.3 - - + -
124A TYR* 3.6 24.9 - + + +
125A LYS 3.2 14.1 - - - +
126A SER* 4.6 0.2 - - - -
147A GLU* 5.0 1.6 - - + -
148A SER* 1.3 77.8 - - - +
150A THR* 1.3 72.3 + - - +
151A VAL* 3.9 14.6 - - + -
163A LYS* 3.4 14.2 + - - +
166A VAL* 3.3 40.7 - - + +
167A ASP* 2.6 32.5 + - - -
170A VAL* 4.3 13.0 - - + -
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Residues in contact with THR 150 (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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28A PHE* 3.6 19.5 - - + +
29A GLU 5.4 0.5 + - - -
34A THR* 3.7 17.8 + - - +
35A CYS 3.4 5.2 - - - -
36A THR* 3.5 22.0 - - - +
123A ASN 3.4 2.9 - - - +
124A TYR* 3.3 4.7 - - - -
125A LYS* 3.0 66.1 + - + +
149A TYR* 1.3 76.0 - - - +
151A VAL* 1.3 65.6 + - - +
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Residues in contact with VAL 151 (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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34A THR* 3.2 3.8 - - - -
35A CYS* 2.9 50.3 + - - +
121A LEU* 3.7 32.3 - - + +
122A LYS 3.7 13.0 - - - +
123A ASN 4.1 2.5 - - - -
124A TYR* 4.0 20.6 - - + -
149A TYR* 3.9 11.9 - - + -
150A THR* 1.3 78.6 + - - +
152A ASP* 1.3 69.1 + - - +
162A THR* 4.2 13.2 - - + -
166A VAL* 4.4 6.1 - - + -
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Residues in contact with ASP 152 (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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33A THR* 3.5 11.3 + - - +
34A THR* 3.6 17.4 - - - +
121A LEU* 4.1 4.9 - - - +
122A LYS* 2.9 37.3 + - + +
123A ASN* 2.6 35.5 + - - +
151A VAL* 1.3 84.2 - - - +
153A ILE* 1.3 66.9 + - - +
154A PRO* 3.4 8.9 - - + +
162A THR* 4.8 0.2 - - - +
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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