Contacts of the strand formed by residues 139 - 149 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B ASN* 4.7 3.1 - - - +
32B PRO* 3.2 24.0 - - + +
44B LEU* 3.8 14.1 - - + -
61B TRP* 3.6 35.2 - - + -
62B VAL 3.3 10.5 - - - +
63B VAL* 3.9 19.3 - - + +
111B PHE* 4.4 3.8 - - + -
125B LEU* 3.9 13.5 - - + -
135B SER 3.3 16.8 + - - +
136B ALA* 3.4 17.6 + - - +
137B ASP 4.4 4.7 - - - +
138B SER* 1.3 78.8 - - - +
140B ARG* 1.3 64.3 + - - +
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Residues in contact with ARG 140 (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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29B GLY* 3.4 33.3 + - - +
30B ILE 3.9 10.6 - - - +
31B ASN* 4.3 16.2 + - - +
32B PRO* 4.0 6.3 - - + -
61B TRP 3.8 0.2 - - - -
62B VAL* 2.8 38.8 + - - +
64B VAL* 4.3 15.9 - - + -
138B SER 4.5 0.2 - - - +
139B VAL* 1.3 75.9 - - - +
141B CYS* 1.3 70.4 + - - +
172B PRO* 3.9 20.2 - - - +
173B ASN 4.9 1.8 + - - -
174B TYR* 3.7 41.4 - - + +
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Residues in contact with CYS 141 (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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29B GLY* 3.3 6.9 - - - -
30B ILE* 2.9 39.8 + - + +
46B CYS* 2.0 51.8 - - + -
59B LEU* 4.0 16.8 - - + -
60B GLU 3.3 4.3 - - - +
61B TRP* 3.5 28.5 - - - -
140B ARG* 1.3 74.3 - - - +
142B ARG* 1.3 60.0 + - - +
143B LEU 3.8 1.3 - - - +
174B TYR* 3.7 6.3 - - - -
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Residues in contact with ARG 142 (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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27B PHE* 3.4 37.0 - - + -
28B LYS 3.5 4.3 - - - +
58B THR 3.3 4.5 - - - +
59B LEU* 4.1 0.2 - - - -
60B GLU* 2.9 61.5 + - + +
62B VAL* 4.2 4.7 - - + -
94B THR* 4.2 14.1 + - - -
95B PRO 5.2 0.6 - - - -
96B MET* 3.5 23.0 - - - +
141B CYS* 1.3 71.4 - - - +
143B LEU* 1.3 65.6 + - - +
144B ARG* 3.6 1.9 + - - +
174B TYR* 3.3 40.8 + - + +
175B GLY* 2.8 28.7 + - - -
177B PRO* 5.2 1.6 - - - +
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Residues in contact with LEU 143 (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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26B TYR 3.0 5.9 - - - +
27B PHE* 3.4 3.5 - - - -
28B LYS* 2.7 42.2 + - + +
30B ILE* 3.8 29.8 - - + -
48B LEU* 3.7 13.2 - - + -
49B PRO* 5.1 0.2 - - + -
57B TRP* 3.7 54.7 - - + -
58B THR 3.8 5.4 - - - +
59B LEU* 4.1 12.1 - - + +
141B CYS* 3.8 2.0 - - + -
142B ARG* 1.3 72.3 - - - +
144B ARG* 1.3 64.2 + - - +
145B MET* 4.0 16.2 - - + +
168B VAL* 4.4 4.9 - - + -
171B LEU* 4.3 14.1 - - + -
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Residues in contact with ARG 144 (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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25B CYS* 3.6 20.0 - - + +
26B TYR 3.4 3.6 - - - -
27B PHE* 3.5 39.4 - - + -
56B SER* 3.2 7.9 + - - +
58B THR* 2.8 51.7 + - - +
94B THR* 5.6 5.1 + - - -
142B ARG* 4.8 2.9 - - - +
143B LEU* 1.3 72.0 - - - +
145B MET* 1.3 59.9 + - - +
146B CYS* 3.3 26.4 + - - +
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Residues in contact with MET 145 (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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25B CYS* 3.3 1.6 - - - -
26B TYR* 2.7 49.6 + - + +
51B VAL* 4.7 0.9 - - + -
53B VAL* 4.5 2.9 - - + -
55B ALA* 3.6 27.4 - - + -
56B SER 3.4 6.7 - - - -
57B TRP* 3.8 32.1 - - + +
143B LEU* 3.7 15.2 - - + -
144B ARG* 1.3 71.8 - - - +
146B CYS* 1.3 58.5 + - - +
147B PRO* 3.8 7.8 - - + +
165B MET* 3.7 31.6 - - + -
168B VAL* 3.7 39.3 - - + -
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Residues in contact with CYS 146 (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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22B PRO* 6.4 1.8 - - + -
24B GLY 3.3 3.8 - - - +
25B CYS* 2.0 47.6 - - - -
55B ALA* 4.1 1.1 - - - -
56B SER* 2.8 44.5 + - - +
144B ARG* 3.3 30.3 - - - -
145B MET* 1.3 75.1 - - - +
147B PRO* 1.4 67.3 - - - +
148B TRP* 3.2 8.5 - - + -
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Residues in contact with PRO 147 (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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179A LEU* 4.9 0.4 - - + -
22B PRO* 3.9 2.3 - - - +
23B LEU* 3.1 36.4 + - + -
24B GLY 3.3 20.4 - - - +
26B TYR* 4.3 13.9 - - + -
53B VAL* 5.3 0.7 - - + -
54B ASN 3.4 12.6 - - - +
55B ALA* 3.8 5.3 - - + -
145B MET* 3.8 11.0 - - - +
146B CYS* 1.4 87.6 - - - +
148B TRP* 1.3 60.6 + - - +
157B PRO* 4.7 6.3 - - + -
161B MET* 4.4 7.0 - - - -
165B MET* 3.8 32.5 - - + -
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Residues in contact with TRP 148 (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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20B ARG* 3.5 64.0 - - + +
21B HIS 3.3 20.2 - - - +
22B PRO* 4.1 3.8 - - + -
23B LEU* 4.1 4.9 - - - +
54B ASN* 2.9 49.8 + - + +
55B ALA* 3.3 30.6 - - - -
56B SER* 3.5 10.3 - - - +
77B GLU* 3.9 10.1 - - - -
78B SER 4.2 7.2 - - - -
146B CYS 3.2 23.8 - - - -
147B PRO* 1.3 74.1 - - - +
149B THR* 1.3 59.9 + - - +
161B MET* 5.3 2.4 - - - +
1F NAG 3.0 38.5 - - - +
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Residues in contact with THR 149 (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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20B ARG* 4.8 2.0 - - - -
21B HIS* 2.9 40.7 + - + +
23B LEU* 3.7 33.8 - - + +
148B TRP* 1.3 74.2 - - - +
150B SER* 1.3 61.5 + - - +
151B ASN* 3.2 35.4 + - - +
154B MET* 3.7 19.7 - - + +
161B MET* 4.8 5.3 - - - +
1F NAG 4.0 11.0 + - - -
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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