Contacts of the helix formed by residues 323 - 336 (chain A) in PDB entry 1D1T
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 LYS 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LEU* 5.2 0.2 - - - -
95A PRO 6.0 0.2 - - - -
96A GLN* 3.2 28.5 - - + +
102A ALA 3.2 9.7 + - - -
103A CYS* 3.2 19.4 + - - +
104A ARG 5.6 0.2 - - - -
105A ASN 2.9 23.1 + - - -
106A PRO* 3.6 19.7 - - - -
108A GLY 2.7 32.4 + - - +
109A ASN* 4.3 6.5 - - + +
321A GLY 3.9 2.2 + - - +
322A LEU* 1.3 69.6 - - - +
324A SER* 1.3 65.7 + - - +
326A ASP* 2.9 22.7 + - + +
327A ASP* 2.9 21.7 + - - +
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Residues in contact with SER 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.4 23.7 - - - +
94A LEU* 2.6 32.8 + - - +
95A PRO 3.4 17.2 + - - -
96A GLN* 3.6 1.7 + - - +
319A PHE* 3.9 22.7 - - - -
322A LEU* 3.2 6.0 + - - -
323A LYS* 1.3 70.7 - - - +
325A ARG* 1.3 58.7 + - - -
328A VAL* 3.1 36.2 + - - +
329A PRO* 3.9 0.2 - - - +
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Residues in contact with ARG 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A THR* 3.8 26.0 - - - +
92A LEU* 3.4 21.5 - - + -
96A GLN* 2.8 44.5 + - + +
97A CYS* 3.8 14.6 + - - +
98A ARG* 3.5 40.9 + - - +
154A GLU* 3.9 7.8 + - - +
155A SER* 3.2 28.5 + - - +
157A VAL 3.4 20.2 - - - +
158A ALA* 4.7 5.2 - - - +
324A SER* 1.3 76.0 + - - +
326A ASP* 1.3 60.0 + - - +
329A PRO* 3.7 15.9 - - - +
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Residues in contact with ASP 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLN* 2.6 34.3 + - - +
98A ARG* 2.9 22.9 + - - +
323A LYS* 2.9 14.8 + - + +
325A ARG* 1.3 78.0 - - - +
327A ASP* 1.3 71.0 + - - +
328A VAL 3.8 0.2 - - - -
329A PRO* 3.6 8.2 - - - +
330A LYS* 3.5 32.2 + - - +
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Residues in contact with ASP 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LYS* 3.6 25.8 + - - -
321A GLY 4.5 0.2 - - - +
322A LEU* 3.3 32.1 - - + +
323A LYS* 2.9 37.5 + - - +
326A ASP* 1.3 82.4 - - - +
328A VAL* 1.3 64.9 + - - +
329A PRO 3.2 2.5 - - - -
330A LYS* 2.8 28.8 + - + +
331A LEU* 2.9 15.2 + - + +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ILE* 3.9 30.5 - - + -
92A LEU* 3.8 17.0 - - + -
158A ALA* 3.9 17.0 - - + -
160A ILE* 4.1 5.4 - - + -
172A ILE* 3.9 17.3 - - + +
177A SER* 5.1 0.9 - - - +
319A PHE* 3.9 27.6 - - + -
322A LEU* 4.8 2.2 - - + +
324A SER* 3.1 15.9 + - - +
327A ASP* 1.3 73.4 - - - +
329A PRO* 1.3 72.0 - - + +
330A LYS 3.1 0.2 + - - -
331A LEU* 3.1 4.1 + - - +
332A VAL* 3.1 21.7 + - - +
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Residues in contact with PRO 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ALA* 4.3 8.5 - - + -
159A LYS 3.4 27.4 - - - +
160A ILE* 4.7 3.8 - - + -
161A ASP 5.7 0.7 + - - -
324A SER 3.9 1.1 - - - +
325A ARG 3.7 19.7 - - - +
326A ASP 3.6 10.1 - - - +
327A ASP 3.5 3.4 - - - -
328A VAL* 1.3 97.2 - - + +
330A LYS* 1.3 56.1 + - + +
332A VAL* 3.6 7.2 + - + +
333A THR* 2.8 31.8 + - - -
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Residues in contact with LYS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ASP* 3.5 27.8 + - - +
327A ASP* 2.8 21.5 + - - +
329A PRO* 1.3 78.1 - - + +
331A LEU* 1.3 61.4 + - + +
333A THR* 3.2 7.3 + - - -
334A GLU* 2.7 44.4 + - - +
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Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ILE* 3.8 13.7 - - + -
176A PHE* 3.9 24.9 - - + -
177A SER* 3.1 35.4 - - - +
180A TYR* 4.1 17.0 - - + -
181A GLY 6.0 0.4 - - - +
322A LEU* 3.8 20.9 - - + -
327A ASP* 2.9 12.4 + - + +
328A VAL 3.7 7.2 - - - +
330A LYS* 1.3 76.7 - - - +
332A VAL* 1.3 56.6 + - - +
334A GLU* 3.3 16.4 + - - +
335A PHE* 2.8 23.7 + - - +
340A PHE* 3.3 21.6 - - + -
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ILE* 4.1 10.1 - - + -
160A ILE* 3.9 28.5 - - + -
161A ASP* 3.9 35.4 - - + +
164A ALA* 4.0 16.2 - - + -
169A VAL* 4.3 6.1 - - + -
172A ILE* 3.8 19.3 - - + -
328A VAL 3.1 15.4 + - - +
329A PRO 3.6 8.7 - - - +
331A LEU* 1.3 74.2 - - - +
333A THR* 1.3 58.1 + - - +
335A PHE* 2.9 20.2 + - - +
336A LEU* 2.9 15.0 + - + +
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Residues in contact with THR 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ASP* 5.1 7.2 + - - +
329A PRO 2.8 21.0 + - - -
330A LYS* 3.2 7.6 + - - -
332A VAL* 1.3 81.3 - - - +
334A GLU* 1.3 58.8 + - + +
336A LEU* 3.3 10.9 + - + +
337A ALA* 3.0 26.5 + - + +
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Residues in contact with GLU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A TYR* 4.4 13.9 + - - -
330A LYS* 2.7 33.4 + - - +
331A LEU* 3.6 20.8 - - - +
333A THR* 1.3 71.3 - - + +
335A PHE* 1.3 67.3 + - - +
337A ALA* 2.9 14.9 + - - -
339A LYS* 3.2 46.1 + - + +
340A PHE* 3.9 12.0 - - + -
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Residues in contact with PHE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PRO* 4.0 25.1 - - + -
168A LYS* 4.2 25.1 - - + -
169A VAL* 3.8 15.3 - - + -
172A ILE* 4.4 2.9 - - + -
331A LEU 2.8 14.6 + - - +
332A VAL* 2.9 11.9 + - - +
334A GLU* 1.3 75.4 - - - +
336A LEU* 1.3 73.6 + - + +
338A LYS* 2.8 24.3 + - - +
340A PHE* 3.7 31.8 - + + +
341A ASP* 4.8 1.8 - - - -
342A LEU* 3.5 42.0 - - + -
343A ASP* 5.8 1.1 - - - -
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Residues in contact with LEU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ASP* 3.1 43.7 - - + +
163A ALA* 4.2 7.0 - - + +
164A ALA* 4.2 8.3 - - + +
165A PRO* 3.9 19.5 - - + -
332A VAL* 2.9 18.0 + - + +
333A THR* 3.6 9.2 - - - +
334A GLU 3.3 0.2 - - - -
335A PHE* 1.3 94.5 - - + +
337A ALA* 1.3 56.9 + - - +
338A LYS* 3.2 8.4 + - - +
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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