Contacts of the helix formed by residues 556 - 575 (chain A) in PDB entry 2YEV
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 556 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A TRP* 3.5 38.1 - + + -
19A LEU* 4.5 8.3 - - + -
20A THR* 4.0 14.3 - - + +
555A SER* 1.3 73.5 + - - +
557A TRP* 1.3 80.1 + + + +
558A PRO* 3.5 1.1 - - - -
559A PHE* 3.3 36.1 + + - +
560A TYR* 3.0 49.8 + + + -
599A GLU* 4.9 0.8 + - - -
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Residues in contact with TRP 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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555A SER* 3.1 11.6 + - - +
556A PHE* 1.3 94.1 - + + +
558A PRO* 1.3 67.5 - - + +
560A TYR* 3.7 44.1 - + + +
561A SER* 2.8 36.6 + - - -
591A TYR* 4.5 9.0 - + - -
592A GLY* 4.2 8.3 - - - +
595A ARG* 3.3 44.0 + - + +
596A TRP* 3.9 34.3 - - + -
599A GLU* 3.7 22.9 + - - +
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Residues in contact with PRO 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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22A VAL* 5.2 1.6 - - + -
108A ARG* 3.6 45.8 - - + +
111A ALA* 4.0 11.2 - - + -
112A PHE* 3.5 25.3 - - + +
115A TRP* 4.5 1.1 - - + -
555A SER* 3.2 23.6 - - - +
556A PHE 3.6 3.8 - - - -
557A TRP* 1.3 90.1 - - + +
559A PHE* 1.3 57.1 + - - +
562A ALA* 3.0 26.0 + - - +
596A TRP* 4.0 16.2 - - + -
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Residues in contact with PHE 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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19A LEU* 3.4 50.8 + - + +
115A TRP* 3.5 45.9 - + + -
556A PHE* 3.3 31.2 + + - +
557A TRP 3.3 0.2 - - - -
558A PRO* 1.3 77.0 - - - +
560A TYR* 1.3 65.7 + - - +
562A ALA* 3.4 1.4 + - - +
563A ALA* 2.9 42.8 + - + +
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Residues in contact with TYR 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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556A PHE* 3.0 41.6 + + + +
557A TRP* 3.3 29.4 + + + +
559A PHE* 1.3 81.5 - - - +
561A SER* 1.3 59.9 + - - +
563A ALA* 3.2 4.9 + - + +
564A THR* 2.9 49.7 + - + +
588A LEU* 3.3 49.9 + - + +
591A TYR* 4.3 9.0 - + - -
592A GLY* 3.5 17.9 - - - -
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Residues in contact with SER 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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112A PHE* 3.8 17.5 - - - -
557A TRP 2.8 22.8 + - - -
558A PRO 3.7 3.8 - - - -
560A TYR* 1.3 76.9 - - - +
562A ALA* 1.3 64.7 + - - +
564A THR* 3.1 9.1 + - - -
565A LEU* 3.0 18.9 + - - +
589A PHE* 3.2 21.1 - - - -
592A GLY* 4.2 11.8 - - - -
593A LEU* 3.5 9.2 + - - +
596A TRP* 3.5 18.6 - - - -
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Residues in contact with ALA 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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112A PHE* 3.5 17.8 - - + -
115A TRP* 3.4 36.4 - - + +
116A ALA* 3.8 16.1 - - - +
119A GLY* 6.0 0.2 - - - -
162A LEU* 5.4 3.2 - - - +
558A PRO 3.0 12.9 + - - +
559A PHE* 3.7 1.3 - - + +
561A SER* 1.3 76.6 - - - +
563A ALA* 1.3 58.4 + - - +
565A LEU* 3.8 3.4 - - - +
566A PHE* 2.8 31.1 + - - +
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Residues in contact with ALA 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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559A PHE* 2.9 36.8 + - + +
560A TYR* 3.5 10.1 - - + +
562A ALA* 1.3 76.6 - - - +
564A THR* 1.3 59.7 + - + +
566A PHE* 3.3 13.2 - - + +
567A ALA* 3.0 27.3 + - - +
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Residues in contact with THR 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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560A TYR* 2.9 50.3 + - + +
561A SER* 3.1 13.0 + - - -
563A ALA* 1.3 77.1 - - + +
565A LEU* 1.3 56.3 + - - +
567A ALA* 3.4 5.7 + - - +
568A PHE* 3.0 22.7 + - - +
585A PHE* 3.6 30.3 - - + +
588A LEU* 4.0 14.1 - - + -
589A PHE* 3.2 21.2 - - - -
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Residues in contact with LEU 565 (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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112A PHE* 4.0 22.0 - - + -
162A LEU* 3.9 20.2 - - + -
165A PHE* 4.5 17.7 - - + -
561A SER 3.0 17.7 + - - +
562A ALA* 3.8 4.5 - - - +
564A THR* 1.3 75.0 + - - +
566A PHE* 1.3 66.9 + - - +
568A PHE* 3.0 21.5 + - + +
569A PHE* 3.0 48.5 + - + -
586A LEU* 5.1 4.0 - - + -
589A PHE* 4.0 28.0 - - + -
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Residues in contact with PHE 566 (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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119A GLY* 3.6 35.9 - - - -
122A VAL* 3.7 28.3 - - + -
123A LEU* 3.8 19.7 - - + -
126A MET* 4.0 7.0 - - + -
162A LEU* 4.2 15.2 - - + +
562A ALA 2.8 19.1 + - - +
563A ALA* 3.3 11.0 - - - +
565A LEU* 1.3 76.5 - - - +
567A ALA* 1.3 63.4 + - + +
569A PHE* 3.0 6.3 + - - +
570A VAL* 2.9 45.6 + - + +
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Residues in contact with ALA 567 (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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563A ALA 3.0 13.4 + - - +
564A THR* 3.6 5.6 - - - +
565A LEU 3.2 0.2 - - - -
566A PHE* 1.3 82.2 - - + +
568A PHE* 1.3 66.0 + - - +
570A VAL* 3.3 8.4 + - - +
571A ALA* 3.0 18.9 + - - +
585A PHE* 3.6 46.7 - - + -
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Residues in contact with PHE 568 (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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564A THR 3.0 14.5 + - - +
565A LEU* 3.0 21.3 + - + +
567A ALA* 1.3 76.5 - - - +
569A PHE* 1.3 88.1 + + - +
571A ALA* 3.3 6.4 + - - +
572A VAL* 3.1 43.2 + - + +
582A MET* 3.5 47.8 - - + -
583A TRP* 5.2 1.1 - + - -
585A PHE* 3.8 14.1 - - + +
586A LEU* 3.7 31.4 - - + +
589A PHE* 6.2 0.2 - - + -
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Residues in contact with PHE 569 (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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123A LEU* 3.7 18.8 - - + -
158A ALA* 3.9 23.9 - - + +
161A LEU* 3.9 36.3 - - + -
162A LEU* 4.1 21.1 - - + -
165A PHE* 4.2 16.8 - + - -
220A LEU* 5.9 1.1 - - + -
565A LEU* 3.0 48.6 + - + -
566A PHE 3.0 7.4 + - - +
568A PHE* 1.3 93.5 - + - +
570A VAL* 1.3 60.7 + - - +
572A VAL* 3.3 11.6 + - + +
573A ALA* 2.8 30.7 + - - +
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Residues in contact with VAL 570 (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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123A LEU* 3.5 21.3 - - + -
126A MET* 4.0 20.0 - - + -
130A PHE* 5.1 3.6 - - + -
155A PHE* 4.9 2.7 - - + -
566A PHE* 2.9 44.6 + - + +
567A ALA* 3.3 9.4 + - - +
569A PHE* 1.3 76.8 - - - +
571A ALA* 1.3 58.5 + - - +
573A ALA* 3.9 2.8 - - - +
574A ALA* 2.8 40.8 + - + +
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Residues in contact with ALA 571 (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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567A ALA 3.0 12.5 + - - +
568A PHE 3.3 8.5 + - - +
570A VAL* 1.3 77.5 - - - +
572A VAL* 1.3 60.7 + - - +
574A ALA* 5.2 0.2 - - - -
575A LEU* 3.4 22.9 + - + +
579A ASN* 3.1 26.6 + - - +
581A TRP* 3.7 31.6 - - + +
582A MET* 3.8 9.4 - - + +
585A PHE* 4.7 2.0 - - + -
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Residues in contact with VAL 572 (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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158A ALA* 5.6 1.8 - - + -
220A LEU* 4.3 27.6 - - + -
224A LYS* 2.9 24.9 + - + -
568A PHE* 3.1 32.7 + - + +
569A PHE* 3.7 15.5 - - + +
570A VAL 3.1 0.2 - - - -
571A ALA* 1.3 75.5 - - - +
573A ALA* 1.3 61.4 + - - +
575A LEU 3.2 5.9 - - - +
577A VAL* 3.9 17.1 - - + +
582A MET* 3.7 31.2 - - + -
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Residues in contact with ALA 573 (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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123A LEU* 5.1 0.7 - - + -
154A ASP* 3.4 41.8 - - - +
155A PHE* 3.9 31.4 - - + -
158A ALA* 4.0 4.9 - - + +
220A LEU* 5.8 0.9 - - - -
224A LYS* 2.9 17.7 + - - -
569A PHE 2.8 18.6 + - - +
570A VAL* 3.9 2.0 - - - +
572A VAL* 1.3 80.2 - - - +
574A ALA* 1.3 58.2 + - - +
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Residues in contact with ALA 574 (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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130A PHE* 3.7 32.0 - - + -
155A PHE* 3.8 12.6 - - + -
224A LYS* 4.6 0.4 - - - -
570A VAL* 2.8 25.4 + - + +
571A ALA* 5.2 0.4 - - - -
573A ALA* 1.3 73.4 - - - +
575A LEU* 1.3 71.6 + - + +
576A PRO* 4.7 0.7 - - - +
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Residues in contact with LEU 575 (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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224A LYS* 3.0 21.1 + - - -
571A ALA* 3.4 25.7 + - + +
572A VAL 3.2 7.3 - - - +
574A ALA* 1.3 92.7 - - + +
576A PRO* 1.3 78.9 - - + +
577A VAL* 3.6 1.2 + - - +
579A ASN* 3.6 18.8 - - + +
581A TRP* 3.9 28.0 - - + -
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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
------------------------------------------------------------
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