Contacts of the strand formed by residues 139 - 149 (chain A) in PDB entry 4PN6
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 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ASN* 4.7 3.1 - - - +
32A PRO* 3.2 24.3 - - + +
44A LEU* 3.8 14.1 - - + -
61A TRP* 3.7 34.5 - - + -
62A VAL 3.3 11.0 - - - +
63A VAL* 3.9 19.5 - - + +
111A PHE* 4.4 3.8 - - + -
125A LEU* 3.9 13.5 - - + -
135A SER 3.4 16.2 - - - +
136A ALA* 3.4 17.4 + - - +
137A ASP 4.4 4.2 - - - +
138A SER* 1.3 78.7 - - - +
140A ARG* 1.3 64.2 + - - +
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Residues in contact with ARG 140 (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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29A GLY* 3.4 34.8 + - - +
30A ILE 3.9 4.5 - - - +
31A ASN* 3.2 31.9 - - - +
32A PRO* 4.0 6.3 - - + -
61A TRP 3.8 0.5 - - - -
62A VAL* 2.8 38.6 + - - +
64A VAL* 4.3 15.3 - - + -
138A SER 4.5 0.4 - - - +
139A VAL* 1.3 75.4 - - - +
141A CYS* 1.3 71.2 + - - +
172A PRO* 4.0 17.8 - - - +
173A ASN 4.9 1.8 + - - -
174A TYR* 3.7 42.9 - - + +
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Residues in contact with CYS 141 (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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29A GLY* 3.3 7.6 - - - -
30A ILE* 2.9 38.3 + - + +
32A PRO* 4.5 0.2 - - - -
46A CYS* 2.0 50.9 - - + -
59A LEU* 4.0 16.6 - - + -
60A GLU 3.4 4.0 - - - +
61A TRP* 3.5 29.6 - - - -
140A ARG* 1.3 74.1 - - - +
142A ARG* 1.3 59.5 + - - +
143A LEU 3.8 1.8 - - - +
174A TYR* 3.7 5.6 - - - -
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Residues in contact with ARG 142 (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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27A PHE* 3.4 34.2 - - - -
28A LYS 3.5 3.8 - - - +
58A THR 3.3 4.3 - - - +
59A LEU* 4.1 0.9 - - - -
60A GLU* 2.9 62.5 + - + +
62A VAL* 4.2 4.3 - - + -
94A THR* 4.2 12.9 + - - -
95A PRO 5.1 0.2 - - - -
96A MET* 3.6 24.0 - - + +
141A CYS* 1.3 71.6 - - - +
143A LEU* 1.3 64.8 + - - +
144A ARG* 3.6 2.3 + - - +
174A TYR* 3.3 42.2 + - + +
175A GLY* 2.7 30.1 + - - -
177A PRO* 4.5 3.6 - - - +
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Residues in contact with LEU 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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26A TYR 3.0 5.9 - - - +
27A PHE* 3.4 3.9 - - - -
28A LYS* 2.7 41.8 + - + +
30A ILE* 3.8 29.6 - - + -
48A LEU* 3.7 12.1 - - + -
49A PRO* 5.0 0.2 - - + -
57A TRP* 3.7 55.6 - - + -
58A THR 3.8 5.2 - - - +
59A LEU* 4.1 11.6 - - + +
141A CYS* 3.8 1.6 - - + -
142A ARG* 1.3 71.9 - - - +
144A ARG* 1.3 64.9 + - - +
145A MET* 4.0 13.9 - - + +
168A VAL* 4.4 4.7 - - + -
171A LEU* 4.3 14.1 - - + -
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Residues in contact with ARG 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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25A CYS* 3.6 19.3 - - + +
26A TYR 3.4 3.4 - - - -
27A PHE* 3.5 39.9 - - + -
56A SER* 3.2 8.0 + - - +
58A THR* 2.8 52.3 + - + +
94A THR* 5.6 5.9 + - - -
142A ARG* 4.8 2.5 - - - +
143A LEU* 1.3 70.9 - - - +
145A MET* 1.3 59.7 + - - +
146A CYS* 3.3 26.4 + - - -
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Residues in contact with MET 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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25A CYS* 3.3 0.7 - - - -
26A TYR* 2.7 50.6 + - + +
51A VAL* 4.6 0.9 - - + -
53A VAL* 4.6 2.7 - - + -
55A ALA* 3.6 28.9 - - + -
56A SER 3.4 6.3 - - - -
57A TRP* 3.8 32.3 - - + +
143A LEU* 3.7 14.7 - - + +
144A ARG* 1.3 71.2 - - - +
146A CYS* 1.3 58.7 + - - +
147A PRO* 3.8 8.0 - - - +
165A MET* 3.7 31.6 - - + -
168A VAL* 3.7 39.0 - - + -
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Residues in contact with CYS 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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22A PRO* 6.4 1.8 - - + -
24A GLY 3.3 3.6 - - - +
25A CYS* 2.0 48.9 - - - -
55A ALA* 3.5 1.2 - - - -
56A SER* 2.8 45.3 + - - +
144A ARG* 3.3 29.8 - - - -
145A MET* 1.3 75.8 - - - +
147A PRO* 1.4 68.5 - - - +
148A TRP* 4.2 3.3 - - - -
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Residues in contact with PRO 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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22A PRO* 3.9 2.8 - - - +
23A LEU* 3.1 35.6 + - + -
24A GLY 3.3 20.4 - - - +
26A TYR* 4.3 13.0 - - + -
53A VAL* 5.4 0.9 - - + -
54A ASN 3.4 12.3 - - - +
55A ALA* 3.8 5.1 - - + -
145A MET* 3.8 12.3 - - - +
146A CYS* 1.4 89.6 - - - +
148A TRP* 1.3 60.6 + - - +
157A PRO* 4.7 6.1 - - + -
161A MET* 4.4 6.7 - - - -
165A MET* 3.7 31.6 - - + -
179B LEU* 5.1 0.4 - - + -
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Residues in contact with TRP 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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20A ARG* 3.4 62.4 - - + +
21A HIS 3.4 19.3 - - - +
22A PRO* 4.3 2.7 - - + -
23A LEU* 3.8 9.1 - - - +
54A ASN* 2.9 61.0 + - + +
55A ALA* 3.4 38.1 - - - -
56A SER* 3.8 11.9 - - - -
77A GLU* 3.3 24.0 - - - -
78A SER 4.1 6.7 - - - -
146A CYS 3.9 3.6 + - - -
147A PRO* 1.3 74.0 - - - +
149A THR* 1.3 68.1 + - - +
161A MET* 4.2 6.9 - - - +
1C NAG 3.3 16.1 + - - +
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Residues in contact with THR 149 (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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19A TYR 3.5 1.1 - - - +
21A HIS* 2.9 38.9 + - + +
23A LEU* 3.8 31.4 - - + -
148A TRP* 1.3 82.9 - - - +
150A SER* 1.3 61.3 + - - +
151A ASN* 3.3 31.3 + - - +
154A MET* 3.8 21.7 - - + +
161A MET* 4.8 3.1 - - - +
1C NAG 3.7 13.5 + - - +
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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