Contacts of the helix formed by residues 273 - 283 (chain 4) in PDB entry 1MVW
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 GLY 273 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1784 LEU* 4.6 1.3 - - - -
2614 LEU 3.8 10.5 - - - -
2624 PHE 4.0 11.7 + - - -
2644 PRO* 4.0 12.2 - - - +
2724 ALA* 1.3 76.5 - - - +
2744 ILE* 1.3 65.6 + - - -
2754 HIS* 3.3 6.6 - - - -
2764 GLU* 2.9 23.3 + - - +
2774 THR* 3.0 12.4 + - - -
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Residues in contact with ILE 274 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1534 LEU* 3.6 27.9 - - + +
1554 SER* 5.7 1.1 - - - +
1604 THR* 3.6 21.1 - - + +
1784 LEU* 3.4 26.0 - - + -
2614 LEU* 3.2 40.1 + - + +
2624 PHE* 3.6 25.8 - - + -
2734 GLY* 1.3 67.5 - - - -
2754 HIS* 1.3 57.8 + - - +
2774 THR* 3.3 7.3 + - + -
2784 THR* 2.9 31.7 + - - -
3094 ILE* 6.2 3.1 - - + -
3134 MET* 3.9 18.4 - - + -
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Residues in contact with HIS 275 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2624 PHE* 3.4 34.9 - + + -
2734 GLY* 2.9 8.0 + - - -
2744 ILE* 1.3 71.4 - - - +
2764 GLU* 1.3 98.0 + - + +
2784 THR* 3.5 3.5 - - - -
2794 TYR* 3.3 21.0 + - - +
3134 MET* 3.4 29.6 - - - -
3164 GLU* 3.2 53.8 + - + -
3174 ILE* 3.8 8.4 - - + +
3204 LEU* 4.9 7.3 - - + +
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Residues in contact with GLU 276 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2724 ALA* 4.1 20.1 - - + +
2734 GLY 2.9 11.1 + - - +
2754 HIS* 1.3 101.1 + - + +
2774 THR* 1.3 53.4 + - - +
2794 TYR* 3.2 7.7 - - - +
2804 ASN* 2.8 50.1 + - - +
3204 LEU* 4.5 14.4 - - + -
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Residues in contact with THR 277 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1604 THR* 6.1 0.4 - - + -
1624 ASN* 2.9 31.4 - - - +
1764 MET* 3.8 19.2 - - + +
1774 ARG 6.0 0.2 - - - -
1784 LEU* 5.2 16.0 - - + +
2724 ALA* 4.0 18.5 + - - +
2734 GLY 3.0 14.3 + - - -
2744 ILE* 3.5 11.4 - - + +
2764 GLU* 1.3 74.2 - - - +
2784 THR* 1.3 64.4 + - - +
2804 ASN* 3.1 7.7 + - - +
2814 SER* 3.1 23.7 + - - -
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Residues in contact with THR 278 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1514 ILE* 3.6 6.9 - - + +
1534 LEU* 3.9 2.6 - - - +
1624 ASN* 3.4 19.4 + - - +
2744 ILE 2.9 15.4 + - - -
2754 HIS 3.5 9.4 - - - -
2774 THR* 1.3 73.3 - - - +
2794 TYR* 1.3 63.8 + - - +
2814 SER* 3.4 4.3 - - - -
2824 ILE* 3.0 36.2 + - + +
2974 ASN* 3.2 34.1 + - - +
3134 MET* 3.0 17.7 - - + +
3174 ILE* 4.1 15.7 - - + -
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Residues in contact with TYR 279 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2754 HIS 3.3 10.5 + - - +
2764 GLU 3.2 8.3 - - - +
2784 THR* 1.3 80.2 - - - +
2804 ASN* 1.3 79.4 + - - +
2824 ILE* 2.9 25.9 + - - +
2834 MET* 2.9 54.6 + - + +
2944 TYR* 3.4 20.4 - + - -
3174 ILE* 5.1 6.3 - - + -
3204 LEU* 3.3 62.6 + - + +
3214 ALA 4.5 0.4 - - - -
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Residues in contact with ASN 280 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1764 MET* 4.8 12.8 - - - -
2724 ALA* 4.9 5.5 - - - +
2764 GLU* 2.8 40.5 + - - +
2774 THR* 3.1 8.8 + - - +
2794 TYR* 1.3 93.4 - - - +
2814 SER* 1.3 61.8 - - - +
2834 MET* 3.2 6.5 + - - +
2844 LYS* 3.1 25.8 + - - +
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Residues in contact with SER 281 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1514 ILE* 3.6 13.2 - - - -
1624 ASN* 3.6 17.7 - - - +
1644 PRO* 3.4 11.8 - - - +
1744 ALA* 2.4 32.1 + - - +
1764 MET* 3.8 7.8 - - - +
2774 THR 3.1 11.2 + - - -
2784 THR 3.4 11.7 - - - -
2804 ASN* 1.3 74.0 - - - +
2824 ILE* 1.3 58.6 + - - +
2844 LYS* 3.1 24.6 + - - +
2854 CYS* 3.4 14.8 + - - -
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Residues in contact with ILE 282 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1514 ILE* 3.7 22.7 - - + -
2784 THR* 3.0 32.8 - - + +
2794 TYR* 2.9 12.5 + - - +
2814 SER* 1.3 80.6 - - - +
2834 MET* 1.3 56.2 + - - +
2844 LYS 3.0 5.3 + - - -
2854 CYS* 3.2 18.5 + - - +
2904 ARG* 3.4 28.3 + - + +
2934 LEU* 4.5 13.0 - - + -
2944 TYR* 3.6 59.2 - - + +
2974 ASN* 4.6 1.8 - - - +
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Residues in contact with MET 283 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2794 TYR* 2.9 57.7 + - + +
2804 ASN* 3.2 7.7 + - - +
2824 ILE* 1.3 68.9 - - - +
2844 LYS* 1.4 55.9 + - - +
2854 CYS 3.5 1.1 - - - +
2904 ARG* 3.9 41.6 + - - +
2944 TYR* 3.4 24.2 - - + +
3224 PRO* 4.0 24.9 - - + -
3254 MET* 6.0 0.9 - - + -
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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