Contacts of the helix formed by residues 315 - 328 (chain 2) in PDB entry 3EXG
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 GLN 315 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2182 HIS* 5.4 2.5 - - - -
3102 ASP* 2.8 34.9 + - + +
3112 ASN* 3.5 26.6 + - - +
3132 ILE* 3.1 6.2 + - + -
3142 PRO* 1.3 74.5 - - - +
3162 VAL* 1.3 67.7 + - - +
3172 LYS* 4.1 15.8 - - + +
3182 ASP* 2.8 39.9 + - - +
3192 ILE* 3.2 13.4 + - - +
351Y ALA* 5.3 1.6 - - - +
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Residues in contact with VAL 316 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2182 HIS* 3.5 34.9 - - + +
2212 GLU* 3.6 30.5 - - + +
2222 ALA* 4.3 11.9 - - - +
2252 VAL* 5.0 4.9 - - + -
3152 GLN* 1.3 71.3 - - - +
3172 LYS* 1.3 65.5 + - - +
3182 ASP 2.9 1.0 + - - -
3192 ILE* 3.1 9.5 + - - +
3202 ILE* 2.9 41.7 + - + +
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Residues in contact with LYS 317 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3152 GLN* 4.1 19.7 - - + +
3162 VAL* 1.3 78.7 - - - +
3182 ASP* 1.4 61.8 + - - +
3202 ILE* 3.1 16.1 + - - +
3212 PHE* 2.9 45.3 + - + +
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Residues in contact with ASP 318 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2952 VAL* 4.4 9.1 - - + +
3152 GLN* 2.8 56.8 + - - +
3172 LYS* 1.4 78.3 - - - +
3192 ILE* 1.3 58.9 + - - +
3212 PHE* 3.3 4.0 + - - +
3222 ALA* 3.0 25.8 + - - +
351Y ALA* 3.6 26.4 - - + +
352Y ASN* 3.3 19.1 + - - +
355Y ILE* 3.5 17.7 - - - +
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Residues in contact with ILE 319 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2092 VAL* 4.9 1.8 - - + -
2152 PRO* 5.7 0.2 - - + -
2182 HIS* 4.3 21.8 - - + +
2192 CYS* 3.8 20.2 - - - -
2222 ALA* 4.1 13.2 - - + -
2602 VAL* 5.1 2.5 - - + -
2622 VAL* 3.6 43.1 - - + -
2952 VAL* 4.2 15.9 - - + -
3142 PRO* 4.6 4.9 - - + -
3152 GLN 3.7 11.2 - - - +
3162 VAL* 3.6 5.6 - - - +
3182 ASP* 1.3 74.9 - - - +
3202 ILE* 1.3 63.6 + - - +
3222 ALA* 4.0 1.1 - - - +
3232 ILE* 3.0 42.9 + - + +
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Residues in contact with ILE 320 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2222 ALA* 4.1 17.3 - - + -
2252 VAL* 3.8 28.5 - - + -
2262 LEU* 3.8 20.9 - - + -
3162 VAL* 2.9 38.0 + - + +
3172 LYS* 3.5 16.8 - - - +
3192 ILE* 1.3 72.6 - - - +
3212 PHE* 1.3 63.7 + - - +
3232 ILE* 4.0 4.9 - - - +
3242 LYS* 3.1 48.5 + - + +
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Residues in contact with PHE 321 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3172 LYS* 2.9 27.6 + - + +
3182 ASP* 3.6 11.0 - - - +
3192 ILE 3.2 0.2 - - - -
3202 ILE* 1.3 77.9 - - - +
3222 ALA* 1.3 58.8 + - - +
3242 LYS* 4.0 4.4 - - + +
3252 LYS* 3.0 62.0 + - + +
352Y ASN* 4.1 10.1 - - - +
354Y TRP* 3.8 34.5 - + + -
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Residues in contact with ALA 322 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2602 VAL* 4.5 4.3 - - + -
2932 VAL* 4.2 11.7 - - + +
2952 VAL* 3.7 24.2 - - + -
3182 ASP 3.0 16.1 + - - +
3192 ILE 4.0 2.0 - - - +
3212 PHE* 1.3 73.8 - - - +
3232 ILE* 1.3 69.0 + - - +
3252 LYS* 3.2 2.1 + - - +
3262 THR* 2.8 28.6 + - - -
352Y ASN* 4.5 2.9 - - + +
354Y TRP* 3.9 23.6 - - + -
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Residues in contact with ILE 323 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2072 ILE* 3.9 28.2 - - + +
2092 VAL* 3.6 26.0 - - + -
2222 ALA* 5.0 3.8 - - + -
2262 LEU* 3.7 37.7 - - + -
2312 VAL* 5.0 1.3 - - + -
2332 CYS* 4.0 6.3 - - - -
2602 VAL* 4.1 12.8 - - + +
3192 ILE* 3.0 33.8 + - + +
3202 ILE 4.0 2.5 - - - +
3222 ALA* 1.3 76.7 - - - +
3242 LYS* 1.3 60.5 + - + +
3262 THR* 3.0 2.9 + - - -
3272 LEU* 2.9 38.8 + - + +
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Residues in contact with LYS 324 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2262 LEU* 4.2 14.4 - - + -
2292 GLU* 3.7 26.4 + - - -
3202 ILE* 3.1 35.9 + - + +
3212 PHE* 4.1 4.7 - - + +
3232 ILE* 1.3 75.1 - - + +
3252 LYS* 1.3 62.6 + - - +
3272 LEU 3.3 0.3 + - - -
3282 ASN* 2.9 20.3 + - - -
3292 ILE* 3.3 53.6 + - + +
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Residues in contact with LYS 325 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3212 PHE* 3.0 47.3 + - + +
3222 ALA 3.6 4.3 - - - +
3242 LYS* 1.3 77.0 - - - +
3262 THR* 1.3 59.7 + - - +
3282 ASN* 3.3 14.0 + - - +
354Y TRP* 3.4 53.3 - - + +
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Residues in contact with THR 326 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2072 ILE* 4.2 7.0 - - + -
2582 HIS* 3.3 40.0 + - + -
2592 LEU 4.3 9.0 - - - +
2602 VAL* 3.8 4.6 - - - +
2902 ALA* 3.4 20.4 - - + +
2912 PRO* 4.2 9.9 + - - +
2932 VAL* 3.0 36.6 - - - +
3222 ALA 2.8 12.2 + - - -
3232 ILE 3.4 8.3 - - - -
3252 LYS* 1.3 70.8 - - - +
3272 LEU* 1.3 59.1 + - - +
3282 ASN* 3.3 2.2 + - - +
354Y TRP* 6.0 0.2 - - - -
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Residues in contact with LEU 327 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2062 HIS* 3.7 25.6 - - + +
2072 ILE* 4.2 8.7 - - + -
2312 VAL* 3.6 30.3 - - + -
2582 HIS* 3.5 39.5 - - + +
3232 ILE* 2.9 24.9 + - + +
3242 LYS 3.3 0.4 + - - +
3262 THR* 1.3 76.3 - - - +
3282 ASN* 1.3 68.0 + - - +
3292 ILE* 2.7 36.3 + - + +
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Residues in contact with ASN 328 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3242 LYS 2.9 9.3 + - - -
3252 LYS* 3.3 9.7 + - - +
3262 THR 3.3 4.8 - - - +
3272 LEU* 1.3 76.1 - - - +
3292 ILE* 1.3 62.7 + - - +
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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