Contacts of the helix formed by residues 2449 - 2462 (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 GLY2449 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2445B GLN 5.8 0.2 + - - -
2448B LYS* 1.3 76.6 - - - +
2450B GLU* 1.3 61.6 + - - +
2451B ALA 3.5 1.3 - - - +
2452B LEU* 3.7 23.4 + - - +
2453B ARG* 4.3 5.5 + - - +
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Residues in contact with GLU2450 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2448B LYS* 3.0 10.8 + - + +
2449B GLY* 1.3 79.1 - - - +
2451B ALA* 1.3 60.5 + - - +
2452B LEU 3.4 0.7 + - - -
2453B ARG* 3.7 33.3 + - - +
2454B ILE* 4.5 3.3 + - - +
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Residues in contact with ALA2451 (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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2439B PRO* 3.9 24.6 - - + +
2444B ILE* 3.3 30.2 + - + +
2448B LYS* 4.7 1.9 - - + +
2449B GLY 3.5 1.4 - - - +
2450B GLU* 1.3 76.0 - - - +
2452B LEU* 1.3 59.5 + - - +
2453B ARG 3.2 1.3 - - - -
2454B ILE* 3.2 15.3 - - + +
2455B ARG* 2.9 30.8 + - + +
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Residues in contact with LEU2452 (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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2444B ILE 5.2 0.8 + - - -
2449B GLY* 3.7 21.7 + - - +
2450B GLU 3.2 1.0 - - - -
2451B ALA* 1.3 77.8 - - - +
2453B ARG* 1.3 57.2 + - - +
2455B ARG* 3.5 13.9 - - - +
2456B ALA* 2.9 31.0 + - - +
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Residues in contact with ARG2453 (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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2449B GLY 4.3 4.8 + - - +
2450B GLU* 3.7 24.9 + - - +
2451B ALA 3.2 0.8 - - - -
2452B LEU* 1.3 79.2 - - - +
2454B ILE* 1.3 73.5 + - + +
2456B ALA* 3.3 5.0 + - - +
2457B ILE* 2.9 39.3 + - + +
174H VAL* 3.8 15.8 + - - +
175H SER* 3.3 26.8 + - - +
176H SER* 4.2 3.1 - - - +
177H GLU* 3.9 26.1 - - - +
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Residues in contact with ILE2454 (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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2348B GLU 5.9 0.9 - - - +
2351B ALA* 5.7 2.5 - - + -
2352B ASN* 5.0 17.0 - - + +
2355B VAL* 4.7 24.9 - - + -
2437B CYS 5.4 3.6 - - - +
2439B PRO* 3.6 27.1 - - + -
2450B GLU 4.8 3.1 - - - +
2451B ALA* 3.2 19.0 - - + +
2453B ARG* 1.3 97.6 - - + +
2455B ARG* 1.3 59.0 - - - +
2457B ILE* 3.5 10.6 - - + +
2458B LEU* 2.9 35.4 + - + +
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Residues in contact with ARG2455 (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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2439B PRO* 3.7 27.4 + - + +
2440B GLU* 5.4 2.0 - - - +
2445B GLN* 3.4 31.8 - - - +
2451B ALA* 2.9 19.1 + - - +
2452B LEU* 3.5 13.1 - - - +
2453B ARG 3.2 0.2 - - - -
2454B ILE* 1.3 78.4 - - - +
2456B ALA* 1.3 58.3 + - - +
2458B LEU* 3.2 17.0 - - + +
2459B ARG* 2.9 31.8 + - + +
2509B ARG 5.4 2.8 + - - -
2510B VAL* 3.6 24.1 + - - +
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Residues in contact with ALA2456 (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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2452B LEU 2.9 16.2 + - - +
2453B ARG* 3.7 5.4 - - - +
2455B ARG* 1.3 78.2 - - - +
2457B ILE* 1.3 64.9 + - + +
2459B ARG* 3.8 5.6 - - - +
2460B SER* 2.9 27.0 + - - -
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Residues in contact with ILE2457 (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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2355B VAL* 6.3 2.7 - - + -
2359B ILE* 4.1 31.9 - - + -
2453B ARG* 2.9 30.4 + - + +
2454B ILE* 3.5 13.0 - - + +
2456B ALA* 1.3 76.8 - - + +
2458B LEU* 1.3 64.7 + - + +
2460B SER* 2.8 20.3 + - - +
2461B LEU* 3.1 14.6 - - + +
131H LEU* 3.7 25.1 - - + -
133H PHE* 5.8 5.8 - - + -
176H SER* 4.2 17.7 - - - +
177H GLU* 6.3 0.4 - - + -
195H PHE* 3.9 15.9 - - + -
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Residues in contact with LEU2458 (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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2355B VAL* 5.4 10.8 - - + -
2434B LEU* 4.8 21.9 - - + +
2437B CYS* 4.6 4.3 - - - +
2438B ALA* 3.7 28.9 - - + +
2439B PRO* 3.8 7.0 - - + -
2454B ILE* 2.9 26.1 + - + +
2455B ARG* 3.2 19.7 - - + +
2457B ILE* 1.3 79.0 - - + +
2459B ARG* 1.3 66.1 + - + +
2461B LEU* 3.7 18.8 + - - +
2462B VAL* 4.0 6.6 + - - +
2506B PHE* 5.2 6.0 - - + -
2510B VAL* 3.6 37.2 - - + +
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Residues in contact with ARG2459 (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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2455B ARG* 2.9 23.1 + - + +
2456B ALA* 4.0 5.4 - - - +
2457B ILE 3.3 0.2 - - - -
2458B LEU* 1.3 81.2 - - + +
2460B SER* 1.3 61.7 + - - +
2461B LEU 3.3 0.2 - - - -
2462B VAL 3.4 15.4 - - - +
2463B PRO* 3.8 3.1 - - - +
2506B PHE* 6.1 0.7 - - - -
2510B VAL* 5.7 4.7 - - + +
2511B TYR* 3.1 43.0 + - + +
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Residues in contact with SER2460 (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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2456B ALA 2.9 14.6 + - - -
2457B ILE* 2.8 19.6 + - - +
2459B ARG* 1.3 76.5 - - - +
2461B LEU* 1.3 63.8 + - - +
2463B PRO* 4.3 9.9 - - - +
130H LYS* 4.6 8.3 - - - +
131H LEU* 3.2 30.0 - - - +
133H PHE* 6.2 4.3 - - - -
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Residues in contact with LEU2461 (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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2359B ILE* 5.0 9.9 - - + -
2365B PHE* 4.9 28.5 - - + -
2370B ARG* 4.5 20.2 - - + -
2377B LEU* 5.6 2.3 - - - +
2434B LEU* 5.3 9.0 - - + -
2457B ILE* 3.1 31.2 - - + +
2458B LEU* 3.9 11.0 - - - +
2459B ARG 3.3 1.0 - - - -
2460B SER* 1.3 85.6 + - - +
2462B VAL* 1.3 70.6 + - + +
2463B PRO* 3.3 7.8 - - - +
130H LYS* 5.1 1.6 - - + -
131H LEU* 3.5 31.0 - - + -
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Residues in contact with VAL2462 (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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2377B LEU* 4.3 22.7 - - + -
2431B ILE* 3.7 28.9 - - + -
2434B LEU* 5.8 6.1 - - + -
2458B LEU 4.0 4.1 + - - +
2459B ARG* 3.4 10.4 + - - +
2461B LEU* 1.3 86.6 - - + +
2463B PRO* 1.3 68.9 - - - +
2466B ASP* 3.6 26.7 - - + -
2467B LEU 4.9 1.6 - - - +
2503B MET* 6.6 0.2 - - + -
2506B PHE* 4.0 23.3 - - + -
2511B TYR* 3.9 9.9 - - - -
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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