Contacts of the helix formed by residues 3429 - 3449 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3420D ASN* 4.4 9.6 + - - +
3423D HIS* 4.2 14.9 - - - +
3424D TRP* 3.9 31.1 - - - +
3427D GLU 4.6 2.1 - - - +
3428D PRO* 1.3 74.9 - - - +
3430D PRO* 1.3 68.6 - - + +
3431D SER* 4.5 2.5 - - - +
3432D ALA* 3.8 23.9 - - + +
3433D GLU* 3.2 20.6 + - - +
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Residues in contact with PRO3430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3428D PRO 3.4 9.8 - - - +
3429D ASN* 1.3 83.8 - - + +
3431D SER* 1.3 59.6 + - - +
3433D GLU* 3.4 6.8 + - + +
3434D GLU* 3.1 27.7 + - - +
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Residues in contact with SER3431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3429D ASN* 3.3 2.4 - - - -
3430D PRO* 1.3 81.1 - - - +
3432D ALA* 1.3 61.1 + - - +
3434D GLU* 3.4 5.5 + - - +
3435D LEU* 2.9 29.9 + - - +
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Residues in contact with ALA3432 (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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3429D ASN* 3.4 26.5 + - + +
3430D PRO 3.3 0.2 - - - -
3431D SER* 1.3 77.8 - - - +
3433D GLU* 1.3 59.2 + - - +
3435D LEU* 3.4 6.8 + - - +
3436D PHE* 3.0 27.7 + - - +
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Residues in contact with GLU3433 (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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3428D PRO* 6.6 0.2 - - + -
3429D ASN 3.2 16.5 + - - +
3430D PRO* 3.8 7.2 - - + +
3432D ALA* 1.3 77.7 - - - +
3434D GLU* 1.3 62.0 + - - +
3436D PHE* 3.4 7.8 + - - +
3437D ARG* 3.3 19.8 + - - +
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Residues in contact with GLU3434 (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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3430D PRO 3.1 17.4 + - - +
3431D SER* 3.9 5.8 - - - +
3433D GLU* 1.3 73.8 - - - +
3435D LEU* 1.3 65.6 + - - +
3437D ARG* 3.3 8.8 + - - +
3438D MET* 3.3 19.8 + - - +
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Residues in contact with LEU3435 (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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3431D SER 2.9 17.9 + - - +
3432D ALA* 3.8 7.9 - - - +
3434D GLU* 1.3 76.9 - - - +
3436D PHE* 1.3 62.5 + - - +
3438D MET* 3.3 8.9 + - - +
3439D VAL* 3.1 21.3 + - - +
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Residues in contact with PHE3436 (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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3432D ALA 3.0 16.9 + - - +
3433D GLU* 3.7 9.2 - - - +
3434D GLU 3.3 0.2 - - - -
3435D LEU* 1.3 78.4 - - - +
3437D ARG* 1.3 58.1 + - - +
3439D VAL* 3.4 7.3 + - - +
3440D GLY* 3.0 23.2 + - - -
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Residues in contact with ARG3437 (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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3433D GLU 3.3 10.2 + - - +
3434D GLU* 3.3 11.8 + - - +
3435D LEU 3.3 0.6 - - - -
3436D PHE* 1.3 76.4 - - - +
3438D MET* 1.3 63.4 + - - +
3440D GLY* 3.2 10.0 + - - +
3441D GLU* 3.3 12.0 + - - +
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Residues in contact with MET3438 (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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3434D GLU 3.3 10.1 + - - +
3435D LEU* 3.7 10.3 - - - +
3436D PHE 3.3 0.8 - - - -
3437D ARG* 1.3 79.5 - - - +
3439D VAL* 1.3 60.8 + - - +
3441D GLU* 3.3 19.4 + - - +
3442D ILE* 3.7 5.9 + - - +
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Residues in contact with VAL3439 (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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3435D LEU 3.1 12.7 + - - +
3436D PHE* 3.4 9.8 + - - +
3437D ARG 3.3 0.2 - - - -
3438D MET* 1.3 76.1 - - - +
3440D GLY* 1.3 57.7 + - - +
3442D ILE* 3.3 8.5 + - - +
3443D PHE* 3.0 25.8 + - - +
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Residues in contact with GLY3440 (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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3436D PHE 3.0 13.9 + - - -
3437D ARG* 3.2 6.7 + - - -
3438D MET 3.2 0.8 - - - -
3439D VAL* 1.3 75.1 - - - +
3441D GLU* 1.3 62.8 + - - +
3443D PHE* 3.2 16.7 + - - +
3444D ILE* 3.3 12.6 + - - +
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Residues in contact with GLU3441 (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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3437D ARG 3.3 8.8 + - - +
3438D MET* 3.3 12.9 + - - +
3439D VAL 3.2 0.6 - - - -
3440D GLY* 1.3 76.8 - - - +
3442D ILE* 1.3 59.8 + - - +
3444D ILE* 3.3 19.3 + - - +
3445D TYR* 3.8 5.5 + - - +
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Residues in contact with ILE3442 (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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3438D MET 3.7 6.3 + - - +
3439D VAL* 3.3 10.6 + - - +
3440D GLY 3.3 0.2 - - - -
3441D GLU* 1.3 76.5 - - - +
3443D PHE* 1.3 59.5 + - - +
3444D ILE 3.2 0.2 - - - -
3445D TYR* 3.3 7.9 + - - +
3446D TRP* 2.9 33.2 + - + +
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Residues in contact with PHE3443 (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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3439D VAL 3.0 13.9 + - - +
3440D GLY* 3.5 14.4 - - - +
3441D GLU 3.2 0.6 - - - -
3442D ILE* 1.3 75.3 - - - +
3444D ILE* 1.3 63.9 + - - +
3446D TRP* 3.3 22.3 + - + +
3447D SER* 4.0 5.4 + - - -
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Residues in contact with ILE3444 (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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3440D GLY 3.3 10.7 + - - +
3441D GLU* 3.6 12.6 - - - +
3442D ILE 3.2 0.6 - - - -
3443D PHE* 1.3 78.4 - - - +
3445D TYR* 1.3 56.3 + - - +
3446D TRP 3.7 0.2 + - - -
3447D SER* 4.3 0.7 + - - -
3448D LYS* 3.3 22.9 + - - +
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Residues in contact with TYR3445 (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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3441D GLU 3.8 5.9 + - - +
3442D ILE* 3.3 9.3 + - - +
3443D PHE 3.3 0.4 - - - -
3444D ILE* 1.3 76.9 - - - +
3446D TRP* 1.3 63.5 + - - +
3447D SER 3.4 1.1 - - - -
3448D LYS* 4.0 9.2 - - - -
3449D SER* 3.4 28.5 + - - +
3452D PHE* 4.5 16.7 - - + +
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Residues in contact with TRP3446 (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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3442D ILE* 2.9 18.6 + - + +
3443D PHE* 3.3 19.6 + - + +
3445D TYR* 1.3 80.3 - - - +
3447D SER* 1.3 64.7 + - - +
3449D SER 3.7 2.3 - - - +
3452D PHE* 5.8 3.1 - - + -
3453D LYS* 3.3 43.9 - - + +
3456D GLU* 4.3 25.4 - - + -
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Residues in contact with SER3447 (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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3443D PHE 4.0 5.3 + - - -
3444D ILE 4.3 0.4 + - - -
3446D TRP* 1.3 83.1 - - - +
3448D LYS* 1.3 66.1 + - - +
3449D SER 3.4 3.9 - - - -
3450D HIS* 4.7 3.3 + - - +
3453D LYS* 5.5 0.7 - - - -
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Residues in contact with LYS3448 (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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3444D ILE 3.3 22.0 + - - +
3445D TYR* 4.0 4.2 - - - -
3446D TRP 3.7 0.2 - - - -
3447D SER* 1.3 80.8 - - - +
3449D SER* 1.3 58.6 + - - +
3450D HIS* 3.6 3.5 + - - +
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Residues in contact with SER3449 (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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3445D TYR* 3.4 19.6 + - - +
3446D TRP 3.7 9.5 - - - +
3447D SER 4.5 2.0 - - - -
3448D LYS* 1.3 75.2 - - - +
3450D HIS* 1.3 64.8 + - - +
3451D ASN* 3.2 3.9 + - - -
3452D PHE* 3.4 34.7 + - - +
3453D LYS 3.5 8.0 + - - -
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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
------------------------------------------------------------
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