Contacts of the strand formed by residues 553 - 564 (chain D) in PDB entry 4JF7
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 PHE 553 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154D THR* 5.9 0.2 - - - -
155D ALA* 5.1 5.0 + - - +
160D GLY 4.3 1.6 + - - -
161D CYS* 4.9 0.6 - - - +
162D THR* 3.4 39.4 + - - +
163D ARG* 4.4 15.5 - - + -
185D CYS* 3.8 24.5 - - + -
520D GLU* 4.4 19.3 - - + -
521D ALA 4.4 2.7 - - - -
522D ALA* 4.2 21.3 - - + -
544D GLU* 3.9 24.2 - - + -
545D LEU 3.3 18.6 - - - -
546D SER* 3.9 19.1 - - - -
547D SER* 4.4 3.6 - - - +
550D LEU 4.6 0.3 - - - +
551D GLY* 4.3 9.5 - - - -
552D GLN* 1.3 91.9 - - + +
554D GLN* 1.3 61.1 + - - +
555D ILE* 5.5 0.2 - - + -
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Residues in contact with GLN 554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D THR* 3.7 35.5 - - + +
162D THR* 4.3 1.1 - - - -
545D LEU* 2.8 41.1 + - + +
547D SER* 4.2 19.9 + - - -
550D LEU 5.0 3.4 - - - +
553D PHE* 1.3 75.8 - - - +
555D ILE* 1.3 64.7 + - - +
556D VAL* 3.6 25.0 + - + +
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Residues in contact with ILE 555 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D SER* 4.8 0.9 + - - -
152D ILE* 3.3 31.9 - - + +
153D PRO 5.4 0.2 - - - +
154D THR* 5.5 1.7 - - - +
162D THR* 3.5 33.1 + - - +
163D ARG* 4.0 6.5 - - - +
165D PRO* 4.2 14.6 - - + -
176D TYR* 3.7 10.5 - - - +
178D HIS* 3.5 35.7 - - + +
542D ILE* 3.5 29.6 - - + -
543D ILE 3.5 9.9 - - - +
544D GLU* 4.3 11.7 - - + +
553D PHE* 5.5 0.2 - - + -
554D GLN* 1.3 76.6 + - - +
556D VAL* 1.3 62.5 + - - +
557D PRO* 4.0 1.0 - - - +
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Residues in contact with VAL 556 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ILE* 4.6 1.1 - - - -
541D TYR 3.1 4.2 - - - +
542D ILE* 3.2 2.3 - - - -
543D ILE 2.8 39.0 + - - +
545D LEU* 4.4 13.0 - - + -
554D GLN* 3.6 37.7 - - + +
555D ILE* 1.3 77.8 - - - +
557D PRO* 1.3 71.8 - - + +
558D PHE* 3.5 43.3 + - + +
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Residues in contact with PRO 557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D MET* 3.8 15.0 - - + +
150D SER* 3.3 39.7 - - - +
151D PHE* 3.9 15.7 - - + -
152D ILE* 3.9 16.2 - - + -
540D ILE* 3.6 23.8 - - + -
541D TYR 3.8 3.8 - - - +
542D ILE* 4.2 5.6 - - + -
555D ILE 4.0 3.4 - - - +
556D VAL* 1.3 89.0 - - + +
558D PHE* 1.3 66.2 + - - +
559D ILE* 3.7 1.4 + - - +
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Residues in contact with PHE 558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D LEU* 3.7 28.9 - - + -
500D MET* 3.7 21.5 - - + -
514D PHE* 3.7 51.6 - + - -
540D ILE* 3.2 5.4 - - - +
541D TYR* 2.9 44.5 + - + +
543D ILE* 3.8 23.1 - - + -
545D LEU* 3.8 9.2 - - + -
556D VAL* 3.6 30.5 - - + -
557D PRO* 1.3 76.3 - - - +
559D ILE* 1.3 60.4 + - - +
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Residues in contact with ILE 559 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D LEU* 3.5 4.0 - - - +
146D LEU* 2.8 56.6 + - + +
148D MET* 3.9 40.4 - - + -
207D PHE* 5.4 0.9 - - + -
208D PRO* 3.8 35.0 - - + +
210D PHE* 4.2 12.1 - - + -
529D PHE* 4.6 2.9 - - + -
538D TYR* 4.4 13.5 - - + -
539D CYS 3.4 13.5 - - - +
540D ILE* 4.7 3.4 - - + -
557D PRO 4.7 0.7 - - - +
558D PHE* 1.3 78.7 - - - +
560D ARG* 1.3 68.2 + - - +
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Residues in contact with ARG 560 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D LEU* 3.8 31.8 - - + +
143D GLY 2.8 34.0 + - - +
144D PRO* 3.4 21.8 - - - +
145D LEU* 3.6 28.6 - - + +
146D LEU* 4.1 5.6 - - - -
500D MET* 3.3 45.7 - - - +
512D GLN* 3.9 29.9 + - - +
538D TYR* 3.4 8.2 - - - -
539D CYS* 2.9 29.1 + - - +
541D TYR* 3.8 16.8 - - + +
559D ILE* 1.3 79.4 - - - +
561D GLN* 1.3 63.1 + - - +
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Residues in contact with GLN 561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D LEU* 3.9 2.4 - - - -
143D GLY* 2.9 29.0 + - - -
144D PRO* 4.5 3.4 + - + -
146D LEU* 4.3 5.2 - - + +
536D MET* 3.1 53.6 - - + +
537D VAL 3.3 14.6 - - - +
538D TYR* 4.0 13.5 - - + -
560D ARG* 1.3 79.4 - - - +
562D VAL* 1.3 67.9 + - - +
563D THR* 3.3 32.2 - - + +
564D LEU 5.4 0.6 - - - +
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Residues in contact with VAL 562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D PHE* 4.0 20.2 - - + -
140D LEU* 4.1 25.8 - - + -
141D THR 3.7 2.5 - - - -
142D LEU* 4.5 1.8 - - + -
469D LEU* 4.3 9.9 - - + -
485D THR* 4.9 0.7 - - - +
502D ILE* 3.8 28.5 - - + -
537D VAL* 2.9 25.1 + - + +
539D CYS* 3.4 33.2 - - + -
541D TYR* 4.2 10.3 - - - +
560D ARG* 3.8 0.6 + - + +
561D GLN* 1.3 79.3 + - - +
563D THR* 1.3 61.1 + - - +
564D LEU 3.9 1.6 + - - -
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Residues in contact with THR 563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D LEU* 3.5 5.9 - - - -
141D THR* 2.9 50.2 + - - +
143D GLY* 4.3 11.5 + - - -
561D GLN* 3.3 49.1 - - + +
562D VAL* 1.3 73.4 - - - +
564D LEU* 1.3 62.7 + - - +
565D SER* 3.4 8.0 + - - -
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Residues in contact with LEU 564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D PHE* 4.3 13.6 - - + -
136D GLU* 3.6 52.3 - - + +
139D ASN* 3.6 21.3 - - + +
140D LEU* 4.0 9.6 - - + +
561D GLN* 5.4 0.8 - - - +
562D VAL 3.9 2.0 + - - -
563D THR* 1.3 71.6 - - - +
565D SER* 1.3 67.1 + - - +
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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