Contacts of the helix formed by residues 413 - 431 (chain D) in PDB entry 2VGB
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 413 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377D MET* 3.5 28.9 + - + +
379D THR 3.9 8.1 - - - -
380D LYS* 3.6 25.1 - - - -
381D PRO* 3.6 29.2 - - + -
407D GLU 4.1 3.6 - - - -
411D GLY 3.3 1.0 - - - -
412D ASN* 1.3 98.9 - - + +
414D PRO* 1.4 62.8 - - - +
415D VAL 3.3 2.0 - - - -
416D GLU* 3.2 37.9 - - + +
417D ALA* 2.9 27.7 + - - +
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Residues in contact with PRO 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ALA* 3.8 23.6 - - + +
103D ARG* 4.3 17.5 - - + +
107D MET* 4.4 10.1 - - - -
407D GLU 3.3 12.8 - - - +
408D THR* 3.7 29.1 - - + +
411D GLY 3.8 9.0 - - - +
412D ASN 3.6 6.1 - - - +
413D PHE* 1.4 87.9 - - - +
415D VAL* 1.3 62.4 + - + +
416D GLU* 4.6 0.9 - - - +
417D ALA* 3.3 4.0 + - - +
418D VAL* 3.0 31.9 + - - +
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Residues in contact with VAL 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ARG* 4.6 18.8 - - + +
106D GLU* 3.7 33.9 - - + +
107D MET* 3.6 26.9 - - + +
110D ALA* 4.3 11.2 - - + -
413D PHE 3.3 0.2 - - - -
414D PRO* 1.3 75.3 - - + +
416D GLU* 1.3 76.0 + - - +
418D VAL* 3.2 4.5 + - - +
419D LYS* 2.8 44.8 + - - +
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Residues in contact with GLU 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LYS* 5.9 0.9 + - - -
377D MET* 3.9 17.3 - - + +
381D PRO* 4.8 5.6 - - + +
412D ASN 4.6 0.2 - - - +
413D PHE* 3.2 45.5 - - + +
414D PRO* 4.0 0.7 - - - +
415D VAL* 1.3 83.6 + - + +
417D ALA* 1.3 56.0 + - - +
419D LYS* 3.1 15.5 + - + +
420D MET* 2.9 29.3 + - - +
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Residues in contact with ALA 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374D LEU* 3.5 11.3 - - + +
377D MET* 3.9 22.5 - - + +
404D LEU* 3.9 10.3 - - + -
407D GLU* 3.9 30.3 - - + +
413D PHE 2.9 17.9 + - - +
414D PRO 3.4 7.0 - - - +
415D VAL 3.2 0.2 - - - -
416D GLU* 1.3 74.9 - - - +
418D VAL* 1.3 61.5 + - - +
420D MET 3.4 0.9 + - - -
421D GLN* 3.2 20.6 + - - +
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Residues in contact with VAL 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D ILE* 3.9 9.5 - - + +
92D ALA* 4.6 5.4 - - + -
107D MET* 4.0 22.2 - - + +
110D ALA* 4.0 5.8 - - + +
111D GLY* 4.0 14.6 - - - +
112D MET* 3.6 29.4 - - + +
404D LEU* 3.7 20.9 - - + -
408D THR* 3.8 9.6 - - + -
414D PRO 3.0 14.7 + - - +
415D VAL* 3.2 6.9 + - - +
417D ALA* 1.3 73.7 - - - +
419D LYS* 1.3 66.1 + - - +
421D GLN* 3.3 3.9 + - - -
422D HIS* 3.0 20.8 + - - +
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Residues in contact with LYS 419 (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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110D ALA* 3.6 21.8 - - + +
415D VAL* 2.8 34.8 + - + +
416D GLU* 3.1 16.1 + - + +
418D VAL* 1.3 76.6 - - - +
420D MET* 1.3 56.9 + - - +
422D HIS* 3.3 11.3 + - + +
423D ALA* 2.9 29.0 + - - +
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Residues in contact with MET 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ALA* 4.3 2.0 - - + -
347B GLU* 3.4 39.3 - - + +
374D LEU* 4.0 10.8 - - + -
377D MET* 4.3 7.2 - - + -
382D ARG* 4.4 13.7 - - - -
383D PRO* 3.8 32.3 - - + -
388D THR* 4.3 4.9 - - - +
416D GLU 2.9 13.2 + - - +
417D ALA 3.7 8.3 - - - +
418D VAL 3.2 0.2 - - - -
419D LYS* 1.3 72.7 - - - +
421D GLN* 1.3 68.7 + - - +
423D ALA* 3.0 3.7 + - + +
424D ILE* 3.0 64.2 + - + +
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Residues in contact with GLN 421 (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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90D ILE* 3.5 29.1 - - + +
373D MET* 4.0 17.2 - - - +
374D LEU* 3.6 18.3 - - + +
391D VAL* 4.3 10.7 - - + +
402D ILE* 3.3 43.4 + - + +
403D MET 3.1 15.4 - - - +
404D LEU* 3.2 22.4 - - + +
417D ALA 3.2 9.7 + - - +
418D VAL 3.9 4.5 - - - +
420D MET* 1.3 74.5 - - - +
422D HIS* 1.3 64.2 + - - +
424D ILE* 3.5 1.4 + - - +
425D ALA* 2.9 27.9 + - - +
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Residues in contact with HIS 422 (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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86D ARG* 2.9 53.1 + - + +
90D ILE* 3.6 6.8 - - + +
110D ALA 3.8 18.5 + - - +
111D GLY* 5.1 0.4 - - - -
418D VAL 3.0 13.6 + - - +
419D LYS* 3.4 11.2 - - + +
421D GLN* 1.3 79.1 - - - +
423D ALA* 1.3 68.6 + - + +
425D ALA 3.4 0.2 + - - -
426D ARG* 3.2 47.1 + - - +
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Residues in contact with ALA 423 (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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347B GLU* 3.2 31.3 - - + +
419D LYS 2.9 19.3 + - - +
420D MET* 3.0 8.2 + - + +
422D HIS* 1.3 81.9 - - + +
424D ILE* 1.3 63.6 + - - +
426D ARG* 3.4 11.9 + - - +
427D GLU* 3.4 17.2 + - - +
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Residues in contact with ILE 424 (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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347B GLU* 4.0 12.3 - - - +
350B PHE* 4.6 7.0 - - + -
374D LEU* 4.4 1.8 - - + -
388D THR* 3.8 21.5 - - + +
391D VAL* 3.6 32.1 - - + -
392D ALA* 3.5 39.0 - - + +
420D MET* 3.0 49.6 + - + +
423D ALA* 1.3 73.7 - - - +
425D ALA* 1.3 65.8 + - - +
427D GLU* 3.1 5.9 + - - +
428D ALA* 3.0 20.6 + - - +
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Residues in contact with ALA 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ARG* 4.3 10.3 - - - +
88D THR* 4.1 14.8 - - - +
391D VAL* 4.5 1.0 - - - +
395D VAL* 4.2 14.8 - - + -
402D ILE* 4.4 8.1 - - + -
421D GLN 2.9 21.9 + - - +
422D HIS 4.0 2.9 - - - +
424D ILE* 1.3 73.6 - - - +
426D ARG* 1.3 57.7 + - - +
428D ALA* 4.5 0.2 - - - -
429D GLU* 2.9 53.0 + - - +
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Residues in contact with ARG 426 (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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82D PRO* 3.9 40.8 + - + +
83D VAL* 4.5 0.8 - - - +
84D ALA 3.1 37.2 + - - +
85D ALA* 4.9 0.4 - - - +
86D ARG* 3.1 28.5 - - + +
422D HIS* 3.2 32.7 + - + +
423D ALA* 3.7 9.2 + - - +
424D ILE 3.1 0.8 - - - -
425D ALA* 1.3 78.3 - - - +
427D GLU* 1.3 63.4 + - - +
429D GLU* 3.9 6.7 - - - +
430D ALA* 3.3 20.3 + - - +
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Residues in contact with GLU 427 (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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347B GLU* 3.7 21.8 - - + +
348B LYS* 2.9 44.3 + - - +
350B PHE* 3.6 19.8 - - + -
351B LEU* 3.4 14.1 - - + +
60D GLN* 4.5 2.6 + - - +
80D SER 4.3 2.9 - - - +
81D GLU* 4.0 0.5 - - - +
82D PRO* 3.1 26.4 - - + +
423D ALA 3.5 13.9 - - - +
424D ILE 3.1 6.8 + - - +
426D ARG* 1.3 77.4 - - - +
428D ALA* 1.3 61.9 + - - +
430D ALA* 3.3 8.6 + - - +
431D ALA* 3.2 19.8 + - - +
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Residues in contact with ALA 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B PHE* 3.5 16.8 - - + -
392D ALA* 3.8 28.0 - - + +
395D VAL* 3.6 22.9 - - + -
396D LEU* 3.4 12.8 - - + +
424D ILE 3.0 15.7 + - - +
425D ALA 4.0 1.1 - - - +
427D GLU* 1.3 76.6 - - - +
429D GLU* 1.3 58.8 + - - +
431D ALA* 2.9 15.7 + - - -
432D VAL* 3.2 8.7 + - - +
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Residues in contact with GLU 429 (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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85D ALA 4.2 1.6 - - - +
86D ARG* 3.1 10.7 - - - +
87D SER* 2.6 42.5 + - - +
88D THR* 2.5 34.4 + - - +
395D VAL* 3.9 8.1 - - + -
425D ALA* 2.9 35.0 + - - +
426D ARG* 3.9 4.9 - - - +
427D GLU 3.3 0.2 - - - -
428D ALA* 1.3 76.1 - - - +
430D ALA* 1.3 60.6 + - - +
432D VAL* 3.2 26.0 + - - +
434D HIS* 4.0 10.7 + - - -
490D ARG* 4.1 0.5 + - - -
510D ARG* 4.9 6.7 - - - +
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Residues in contact with ALA 430 (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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59D GLN* 3.2 39.0 - - + +
60D GLN* 3.3 15.3 - - + +
64D ALA* 5.9 0.2 - - - +
72D HIS* 5.6 0.3 - - - -
80D SER 6.0 0.4 - - - +
82D PRO* 4.7 11.7 - - + -
83D VAL 5.8 0.2 - - - +
426D ARG 3.3 9.9 + - - +
427D GLU* 3.3 12.8 + - - +
429D GLU* 1.3 77.1 - - - +
431D ALA* 1.3 59.4 + - - +
432D VAL 3.3 1.5 - - - +
490D ARG* 3.3 17.7 + - - +
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Residues in contact with ALA 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B PHE* 4.6 2.5 - - + -
351B LEU* 3.9 15.5 - - + -
60D GLN* 4.3 1.8 - - + -
72D HIS* 2.9 21.5 + - - -
76D LEU* 3.8 28.9 - - + -
396D LEU* 4.1 13.3 - - + +
427D GLU 3.2 11.1 + - - +
428D ALA* 2.9 14.3 + - - +
430D ALA* 1.3 77.4 - - - +
432D VAL* 1.3 64.7 + - - +
433D TYR 3.3 0.2 + - - -
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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
------------------------------------------------------------
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