Contacts of the helix formed by residues 3429 - 3449 (chain B) in PDB entry 6X34
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 ASN3429 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3420B ASN* 4.4 9.4 + - - +
3423B HIS* 4.2 14.3 - - - +
3424B TRP* 3.9 31.3 - - - +
3427B GLU 4.6 2.1 - - - +
3428B PRO* 1.3 74.5 - - - +
3430B PRO* 1.3 68.8 - - + +
3431B SER* 4.5 2.5 - - - +
3432B ALA* 3.8 24.1 - - + +
3433B GLU* 3.2 21.0 + - - +
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Residues in contact with PRO3430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3428B PRO 3.4 9.4 - - - +
3429B ASN* 1.3 83.6 - - + +
3431B SER* 1.3 58.9 + - - +
3433B GLU* 3.4 6.8 + - + +
3434B GLU* 3.1 28.1 + - - +
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Residues in contact with SER3431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3429B ASN* 3.3 2.6 - - - +
3430B PRO* 1.3 80.7 - - - +
3432B ALA* 1.3 60.6 + - - +
3434B GLU* 3.4 5.7 + - - +
3435B LEU* 2.9 29.3 + - - +
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Residues in contact with ALA3432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3429B ASN* 3.4 25.6 + - + +
3430B PRO 3.3 0.4 - - - -
3431B SER* 1.3 76.8 - - - +
3433B GLU* 1.3 59.3 + - - +
3435B LEU* 3.4 6.6 + - - +
3436B PHE* 3.0 28.1 + - - +
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Residues in contact with GLU3433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3428B PRO* 6.6 0.2 - - + -
3429B ASN 3.2 15.5 + - - +
3430B PRO* 3.8 7.6 - - + +
3431B SER 3.3 0.2 - - - -
3432B ALA* 1.3 78.2 - - - +
3434B GLU* 1.3 60.9 + - - +
3436B PHE* 3.4 7.6 + - - +
3437B ARG* 3.3 19.8 + - - +
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Residues in contact with GLU3434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3430B PRO 3.1 18.3 + - - +
3431B SER* 3.9 5.8 - - - +
3433B GLU* 1.3 74.0 - - - +
3435B LEU* 1.3 65.1 + - - +
3437B ARG* 3.3 8.6 + - - +
3438B MET* 3.3 19.2 + - - +
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Residues in contact with LEU3435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3431B SER 2.9 18.3 + - - +
3432B ALA* 3.8 7.4 - - - +
3433B GLU 3.3 0.2 - - - -
3434B GLU* 1.3 76.5 - - - +
3436B PHE* 1.3 62.0 + - - +
3438B MET* 3.3 8.8 + - - +
3439B VAL* 3.1 21.8 + - - +
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Residues in contact with PHE3436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3432B ALA 3.0 17.6 + - - +
3433B GLU* 3.7 8.3 - - - +
3434B GLU 3.3 0.4 - - - -
3435B LEU* 1.3 78.1 - - - +
3437B ARG* 1.3 55.3 + - - +
3439B VAL* 3.4 7.8 + - - +
3440B GLY* 3.0 23.7 + - - -
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Residues in contact with ARG3437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3433B GLU 3.3 9.7 + - - +
3434B GLU* 3.3 10.7 + - - +
3435B LEU 3.3 0.8 - - - -
3436B PHE* 1.3 76.9 - - - +
3438B MET* 1.3 63.3 + - - +
3440B GLY* 3.2 10.1 + - - +
3441B GLU* 3.3 11.8 + - - +
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Residues in contact with MET3438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3434B GLU 3.3 10.5 + - - +
3435B LEU* 3.7 11.4 - - - +
3436B PHE 3.3 0.4 - - - -
3437B ARG* 1.3 80.3 - - - +
3439B VAL* 1.3 61.8 + - - +
3441B GLU* 3.3 18.4 + - - +
3442B ILE* 3.7 6.2 + - - +
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Residues in contact with VAL3439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3435B LEU 3.1 13.2 + - - +
3436B PHE* 3.8 9.9 - - - +
3437B ARG 3.3 0.2 - - - -
3438B MET* 1.3 75.6 - - - +
3440B GLY* 1.3 59.2 + - - +
3442B ILE* 3.3 9.0 + - - +
3443B PHE* 3.0 25.6 + - - +
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Residues in contact with GLY3440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3436B PHE 3.0 14.4 + - - -
3437B ARG* 3.2 5.8 + - - -
3438B MET 3.2 0.8 - - - -
3439B VAL* 1.3 75.6 - - - +
3441B GLU* 1.3 63.2 + - - +
3443B PHE* 3.2 16.8 + - - +
3444B ILE* 3.3 12.6 + - - +
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Residues in contact with GLU3441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3437B ARG 3.3 9.0 + - - +
3438B MET* 3.3 12.7 + - - +
3439B VAL 3.2 0.4 - - - -
3440B GLY* 1.3 77.3 - - - +
3442B ILE* 1.3 59.7 + - - +
3444B ILE* 3.3 18.8 + - - +
3445B TYR* 3.8 6.4 + - - +
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Residues in contact with ILE3442 (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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3438B MET 3.7 6.9 + - - +
3439B VAL* 3.3 10.4 + - - +
3440B GLY 3.3 0.2 - - - -
3441B GLU* 1.3 77.4 - - - +
3443B PHE* 1.3 59.9 + - - +
3445B TYR* 3.3 7.7 + - - +
3446B TRP* 2.9 33.9 + - + +
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Residues in contact with PHE3443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3439B VAL 3.0 13.9 + - - +
3440B GLY* 3.5 14.1 - - - +
3441B GLU 3.2 0.6 - - - -
3442B ILE* 1.3 76.5 - - - +
3444B ILE* 1.3 63.1 + - - +
3446B TRP* 3.3 23.1 + - + +
3447B SER* 4.0 5.0 + - - -
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Residues in contact with ILE3444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3440B GLY 3.3 10.1 + - - +
3441B GLU* 3.6 12.1 - - - +
3442B ILE 3.2 0.8 - - - -
3443B PHE* 1.3 78.5 - - - +
3445B TYR* 1.3 57.1 + - - +
3447B SER* 5.4 0.5 - - - -
3448B LYS* 3.3 23.0 + - - +
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Residues in contact with TYR3445 (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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3441B GLU 3.8 6.5 + - - +
3442B ILE* 3.3 10.3 + - - +
3444B ILE* 1.3 76.8 - - - +
3446B TRP* 1.3 63.6 + - - +
3447B SER 3.4 1.3 - - - -
3448B LYS* 4.0 8.3 - - - -
3449B SER* 3.4 29.3 + - - +
3452B PHE* 4.5 16.4 - - + +
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Residues in contact with TRP3446 (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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3442B ILE* 2.9 18.6 + - + +
3443B PHE* 3.3 19.1 + - + +
3445B TYR* 1.3 80.4 - - - +
3447B SER* 1.3 63.3 + - - +
3449B SER 3.7 2.1 - - - +
3452B PHE* 5.8 3.6 - - + -
3453B LYS* 3.3 44.5 - - + +
3456B GLU* 4.3 25.1 - - + -
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Residues in contact with SER3447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3443B PHE 4.0 6.1 + - - -
3444B ILE 5.4 0.7 - - - -
3446B TRP* 1.3 83.2 - - - +
3448B LYS* 1.3 65.4 + - - +
3449B SER 3.4 3.6 - - - -
3450B HIS* 4.7 3.5 + - - +
3453B LYS* 5.5 1.1 - - - -
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Residues in contact with LYS3448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3444B ILE 3.3 22.2 + - - +
3445B TYR* 4.3 3.6 - - - -
3446B TRP 3.7 0.2 - - - -
3447B SER* 1.3 79.8 - - - +
3449B SER* 1.3 58.9 + - - +
3450B HIS* 3.6 3.5 + - - +
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Residues in contact with SER3449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3445B TYR* 3.4 19.4 + - - +
3446B TRP 3.7 10.2 - - - +
3447B SER 4.5 1.8 - - - -
3448B LYS* 1.3 76.9 - - - +
3450B HIS* 1.3 64.9 + - - +
3451B ASN* 3.2 3.2 + - - -
3452B PHE* 3.4 34.5 + - - -
3453B LYS 3.5 8.1 + - - -
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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
------------------------------------------------------------
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