Contacts of the strand formed by residues 137 - 145 (chain B) in PDB entry 3FN3
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 ILE 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A GLN 4.6 4.8 + - - -
140A ARG* 3.8 11.3 - - + +
141A ILE 3.7 15.4 + - - +
134B TYR 4.1 21.1 - - - +
135B ASN* 3.5 8.5 + - - +
136B LYS* 1.3 73.5 - - - +
138B ASN* 1.3 70.5 + - - +
139B GLN* 5.0 3.5 - - + +
155B CYS* 4.3 1.3 - - - -
156B GLN 3.5 6.3 - - - +
157B ALA* 4.2 8.1 - - + -
209B CYS* 4.2 5.8 - - - -
211B PHE* 3.7 31.9 - - + -
220B HIS* 4.3 8.1 - - + +
221B THR 3.9 17.0 - - - +
222B ALA* 3.9 33.4 - - + -
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Residues in contact with ASN 138 (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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139A GLN* 5.1 3.1 + - - -
140A ARG 4.8 0.2 - - - -
141A ILE* 3.1 37.9 - - + +
225A VAL 4.6 4.0 + - - -
227A PRO* 3.5 42.1 - - + +
229A LEU* 5.0 4.7 - - + +
136B LYS* 4.3 11.6 + - - +
137B ILE* 1.3 76.5 - - - +
139B GLN* 1.3 63.2 + - - +
155B CYS* 3.3 3.5 - - - -
156B GLN* 2.8 47.5 + - + +
157B ALA* 5.4 1.2 - - - +
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Residues in contact with GLN 139 (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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140A ARG* 4.2 17.8 + - - +
141A ILE 3.0 14.3 + - - +
142A LEU* 3.4 32.6 - - + +
143A VAL* 3.1 27.5 + - - +
229A LEU* 4.9 3.2 - - - +
137B ILE* 5.0 5.2 - - + +
138B ASN* 1.3 76.4 - - - +
140B ARG* 1.3 60.2 + - - +
141B ILE* 4.4 6.9 - - - +
154B THR 3.2 10.8 - - - +
155B CYS* 4.3 10.1 - - - -
222B ALA* 4.7 8.3 - - - +
223B GLU 3.1 26.2 + - - +
224B LEU* 3.9 23.1 - - + +
225B VAL 4.8 2.0 - - - +
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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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142A LEU* 4.3 0.7 - - - -
143A VAL* 3.6 35.1 - - + +
146A PRO* 4.4 19.3 - - + +
229A LEU* 4.1 18.5 + - + +
230A PRO* 3.0 37.8 + - - +
231A LEU* 3.8 10.3 + - - +
232A ALA* 5.4 1.4 - - - +
139B GLN* 1.3 74.3 - - - +
141B ILE* 1.3 76.0 + - - +
142B LEU* 3.9 27.9 - - + +
152B GLU* 3.5 20.6 + - - -
153B LEU* 3.3 5.0 - - - +
154B THR* 2.8 54.6 + - - +
224B LEU* 4.3 0.9 - - - +
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Residues in contact with ILE 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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142A LEU* 4.4 16.8 - - + +
143A VAL 4.5 0.5 + - - +
144A VAL 4.7 9.9 - - - +
139B GLN* 4.4 5.2 - - - +
140B ARG* 1.3 82.9 - - - +
142B LEU* 1.3 67.6 + - - +
143B VAL* 5.8 0.5 - - - +
151B HIS* 4.4 10.1 - - + -
152B GLU 3.4 2.0 - - - -
153B LEU* 3.6 20.9 - - + -
224B LEU* 3.7 30.5 - - + -
225B VAL 3.5 29.4 - - - +
226B ILE* 3.9 11.0 - - + -
227B PRO* 3.9 24.4 - - + +
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Residues in contact with LEU 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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144A VAL 5.8 0.4 - - - +
146A PRO* 3.8 34.3 - - + -
231A LEU 5.5 3.6 - - - +
140B ARG* 3.9 25.1 - - + +
141B ILE* 1.3 80.4 - - - +
143B VAL* 1.3 65.4 - - + +
144B VAL* 4.7 4.7 - - + +
151B HIS* 3.0 13.7 - - - +
152B GLU* 2.6 68.2 + - + +
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Residues in contact with VAL 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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141B ILE 5.8 0.7 - - - +
142B LEU* 1.3 74.4 - - + +
144B VAL* 1.3 61.6 + - - +
145B ASP 4.1 1.3 - - - +
146B PRO* 3.8 38.6 - - + +
150B GLU 3.8 2.5 - - - +
151B HIS* 3.8 20.9 - - + +
227B PRO* 6.5 1.3 - - + -
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Residues in contact with VAL 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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142B LEU* 3.4 7.1 + - + +
143B VAL* 1.3 74.0 - - - +
145B ASP* 1.3 60.0 + - + +
146B PRO* 4.5 1.2 - - - +
150B GLU* 3.1 27.7 + - - +
151B HIS 4.2 1.1 - - - -
152B GLU* 3.7 32.1 - - + +
198B ARG* 3.2 44.4 - - - +
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Residues in contact with ASP 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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143B VAL* 3.3 3.4 + - - -
144B VAL* 1.3 88.3 - - + +
146B PRO* 1.3 70.6 - - - +
147B VAL* 3.2 22.2 + - - +
148B THR* 3.3 28.2 + - - +
149B SER* 2.9 17.2 + - - -
150B GLU* 3.2 17.8 + - + +
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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