Contacts of the strand formed by residues 553 - 564 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ALA* 5.5 1.4 - - - +
160A GLY 4.0 3.1 + - - +
161A CYS* 4.0 3.2 - - - -
162A THR* 3.2 34.2 + - - +
163A ARG* 4.0 17.5 - - - -
185A CYS* 3.8 27.3 - - + -
520A GLU* 3.8 30.1 - - + -
521A ALA 4.3 8.1 - - - -
522A ALA* 4.1 11.4 - - + -
544A GLU* 3.9 23.6 - - + -
545A LEU 3.3 30.5 - - - -
546A SER* 4.2 12.8 - - - -
547A SER* 4.2 2.0 - - - +
551A GLY* 4.7 3.2 - - - -
552A GLN* 1.3 87.9 + - + +
554A GLN* 1.3 61.8 + - - +
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Residues in contact with GLN 554 (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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154A THR* 3.8 34.3 - - + +
162A THR* 3.7 3.1 - - - -
544A GLU* 3.4 5.9 - - - +
545A LEU* 2.9 43.7 + - + +
546A SER 4.8 0.9 - - - +
547A SER* 3.9 26.5 + - - -
550A LEU 5.2 3.3 + - - +
553A PHE* 1.3 73.8 - - - +
555A ILE* 1.3 69.2 + - - +
556A VAL* 4.2 21.2 - - + +
154B THR* 5.1 7.5 + - - +
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Residues in contact with ILE 555 (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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150A SER* 4.9 0.2 + - - -
152A ILE* 3.3 32.4 - - + +
153A PRO 5.7 1.0 + - - -
154A THR* 5.2 3.5 - - - +
162A THR* 3.6 25.6 + - - +
163A ARG* 4.0 12.3 - - - -
165A PRO* 3.8 26.2 - - + -
176A TYR* 3.7 20.9 - - - +
178A HIS* 4.0 9.9 - - + +
542A ILE* 3.5 30.5 - - + -
543A ILE 3.5 7.4 - - - +
544A GLU* 4.0 9.6 - - + +
554A GLN* 1.3 84.4 - - - +
556A VAL* 1.3 66.5 + - - +
557A PRO* 4.1 0.7 - - - +
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Residues in contact with VAL 556 (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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150A SER* 5.8 0.4 - - - -
152A ILE* 4.5 2.0 - - - -
154A THR* 6.2 0.7 - - + -
541A TYR 3.2 4.7 - - - +
542A ILE* 3.3 2.1 - - - -
543A ILE 2.9 32.2 + - - +
545A LEU* 3.9 19.7 - - + -
554A GLN* 4.2 23.3 - - + +
555A ILE* 1.3 79.2 - - - +
557A PRO* 1.3 74.3 - - + +
558A PHE* 3.5 37.9 + - + -
154B THR* 6.0 2.2 - - - +
155B ALA 5.1 2.2 - - - +
156B THR* 4.6 13.7 - - + -
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Residues in contact with PRO 557 (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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148A MET* 4.1 8.7 - - + +
150A SER* 3.1 44.2 - - - +
151A PHE* 3.7 29.2 - - + -
152A ILE* 4.0 14.8 - - + -
540A ILE* 3.9 10.8 - - + -
541A TYR 3.9 2.9 - - - +
542A ILE* 4.2 7.6 - - + -
555A ILE 4.1 1.1 - - - +
556A VAL* 1.3 88.5 - - + +
558A PHE* 1.3 64.8 + - - +
559A ILE* 3.7 1.2 + - - +
156B THR* 3.4 15.7 - - + +
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Residues in contact with PHE 558 (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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145A LEU* 3.9 19.3 - - + -
500A MET* 3.7 20.6 - - + -
514A PHE* 3.8 48.5 - + - -
539A CYS 3.8 0.2 - - - +
540A ILE* 3.1 5.9 - - - +
541A TYR* 2.7 49.9 + - + +
543A ILE* 3.6 26.2 - - + -
545A LEU* 4.0 12.3 - - + -
556A VAL* 3.7 28.3 - - + -
557A PRO* 1.3 74.2 - - - +
559A ILE* 1.3 59.5 + - - +
156B THR* 3.7 24.5 - - - -
157B THR* 5.7 0.4 - - - -
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Residues in contact with ILE 559 (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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145A LEU* 3.6 6.2 - - - +
146A LEU* 2.9 56.8 + - + +
148A MET* 4.0 35.7 - - + -
207A PHE* 5.1 2.0 - - + -
208A PRO* 3.7 41.5 - - + -
210A PHE* 4.3 10.8 - - + -
529A PHE* 4.5 2.9 - - + -
538A TYR* 4.3 10.5 - - + -
539A CYS 3.5 13.7 - - - +
540A ILE* 4.7 2.9 - - + -
557A PRO 3.7 1.2 + - - -
558A PHE* 1.3 75.4 - - - +
560A ARG* 1.3 72.2 + - - +
156B THR* 4.9 1.0 + - - +
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Residues in contact with ARG 560 (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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142A LEU* 3.7 33.5 - - + +
143A GLY 2.6 34.7 + - - +
144A PRO* 3.4 20.7 - - - +
145A LEU* 3.6 28.6 - - + +
146A LEU* 4.2 5.2 - - - -
500A MET* 3.4 38.8 - - - +
512A GLN* 3.8 33.9 + - - +
513A GLN 5.9 0.2 + - - -
514A PHE* 6.0 0.4 - - - +
538A TYR* 3.5 7.4 - - - -
539A CYS* 2.9 30.5 + - - +
541A TYR* 3.8 16.1 - - + -
559A ILE* 1.3 80.1 - - - +
561A GLN* 1.3 62.9 + - - +
562A VAL* 5.9 0.2 - - + -
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Residues in contact with GLN 561 (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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142A LEU* 3.8 2.8 - - - -
143A GLY* 2.8 30.2 + - - +
144A PRO* 4.6 2.9 + - + -
146A LEU* 4.3 5.7 - - + +
536A MET* 3.2 49.1 - - + +
537A VAL 3.3 13.9 - - - +
538A TYR* 4.1 15.9 + - + -
560A ARG* 1.3 77.8 - - - +
562A VAL* 1.3 67.3 + - - +
563A THR* 3.6 31.1 + - + +
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Residues in contact with VAL 562 (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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132A PHE* 4.1 12.7 - - + -
140A LEU* 4.0 26.2 - - + -
141A THR 3.6 2.7 - - - -
142A LEU* 4.5 2.5 - - + -
469A LEU* 4.3 8.7 - - + -
485A THR* 5.0 0.4 - - - +
502A ILE* 3.8 29.6 - - + -
537A VAL* 2.8 35.5 + - + +
539A CYS* 3.6 31.4 - - + -
541A TYR* 4.4 10.5 - - - +
560A ARG* 3.9 0.6 + - + +
561A GLN* 1.3 77.5 + - - +
563A THR* 1.3 62.2 + - - +
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Residues in contact with THR 563 (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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140A LEU* 3.3 9.0 - - - -
141A THR* 3.0 42.9 + - - +
142A LEU 4.9 0.4 - - - -
143A GLY* 4.3 11.9 - - - +
561A GLN* 3.6 40.8 - - + +
562A VAL* 1.3 78.1 - - - +
564A LEU* 1.3 62.2 + - - +
565A SER* 3.5 9.7 + - - -
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Residues in contact with LEU 564 (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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132A PHE* 4.1 14.2 - - + -
136A GLU* 3.4 61.2 - - + +
139A ASN* 3.8 12.6 - - + +
140A LEU* 4.0 11.1 - - + +
562A VAL 4.2 0.4 + - - -
563A THR* 1.3 74.2 + - - +
565A SER* 1.3 75.8 + - - +
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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