Contacts of the helix formed by residues 57 - 73 (chain B) in PDB entry 4ND1
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 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A ASP 5.5 0.2 - - - -
242A ASN* 3.0 33.8 - - - +
244A LYS* 5.6 0.2 - - - -
56B GLU* 1.3 70.5 - - - +
58B ILE* 1.3 54.7 + - - -
60B GLN* 2.9 23.3 + - - +
61B GLY 2.7 31.9 + - - -
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Residues in contact with ILE 58 (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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242A ASN 3.2 4.8 + - - +
243A LEU* 3.1 34.3 - - + +
244A LYS* 4.5 11.0 - - + -
29B SER* 3.6 26.5 - - - +
30B GLY* 5.5 0.4 - - - -
53B ASP* 4.8 3.8 - - - +
55B ALA* 4.2 18.8 - - + +
56B GLU 3.0 12.9 + - - +
57B GLY* 1.3 73.0 - - - +
59B PRO* 1.3 72.4 - - + +
61B GLY* 3.4 0.7 + - - -
62B LYS* 3.1 37.9 + - - +
401B NAD 5.1 3.4 - - - +
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Residues in contact with PRO 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B SER* 3.5 22.2 - - - +
51B LEU* 3.4 27.4 - - + +
53B ASP* 3.7 19.1 - - + +
55B ALA 3.3 15.7 - - - +
58B ILE* 1.3 96.5 - - + +
60B GLN* 1.3 69.9 + - - +
62B LYS* 4.7 1.8 - - + +
63B ALA* 3.1 28.9 + - - +
80B GLY* 3.4 6.2 - - - -
81B THR 3.8 13.7 - - - +
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Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ASN* 4.0 14.4 - - - +
55B ALA 5.6 0.4 + - - -
56B GLU* 5.7 1.0 - - - +
57B GLY* 3.0 32.5 + - - +
59B PRO* 1.3 82.1 - - - +
61B GLY* 1.3 65.8 + - - +
63B ALA* 3.5 2.1 + - - +
64B LEU* 3.0 35.4 + - + +
80B GLY* 4.0 15.9 + - - +
81B THR* 3.7 29.5 - - - +
83B ASN* 4.2 8.5 - - - +
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Residues in contact with GLY 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A VAL* 4.0 10.0 - - - +
242A ASN* 3.4 23.5 - - - +
243A LEU* 3.8 14.4 - - - -
57B GLY 2.7 15.8 + - - -
58B ILE 3.8 1.6 - - - -
60B GLN* 1.3 73.7 - - - +
62B LYS* 1.3 60.7 + - - +
64B LEU* 3.5 5.1 + - - +
65B ASP* 3.1 24.3 + - - +
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.7 15.5 - - + -
247A TYR* 3.5 19.8 + - - +
248A PHE* 4.1 14.8 - - + -
29B SER* 2.7 32.2 + - - +
30B GLY* 2.9 24.5 + - - -
31B GLN* 4.6 7.1 - - - +
34B GLY* 4.3 14.7 - - - -
51B LEU* 4.2 10.1 - - + -
58B ILE* 3.1 26.2 + - - +
59B PRO 4.2 2.9 - - - +
61B GLY* 1.3 73.0 - - - +
63B ALA* 1.3 60.4 + - - +
65B ASP* 3.4 5.1 + - - +
66B ILE* 2.8 38.9 + - + +
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Residues in contact with ALA 63 (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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51B LEU* 4.0 3.3 - - + +
59B PRO 3.1 20.2 + - - +
60B GLN 3.9 3.4 - - - +
61B GLY 3.4 0.2 - - - -
62B LYS* 1.3 77.2 - - - +
64B LEU* 1.3 50.0 + - + +
66B ILE* 3.7 0.7 - - - +
67B THR* 2.7 42.9 + - - -
78B VAL* 3.6 24.4 - - + +
79B ILE* 3.4 10.3 - - - +
80B GLY 3.4 22.9 - - - +
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Residues in contact with LEU 64 (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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175A PHE* 6.1 3.1 - - + -
178A GLN* 6.0 2.7 - - - +
231A HIS* 6.1 1.8 - - + +
238A GLU* 3.7 42.8 - - + +
239A VAL* 4.4 10.1 - - + -
242A ASN* 4.1 14.4 - - - +
60B GLN* 3.0 24.6 + - + +
61B GLY* 3.8 5.4 - - - +
62B LYS 3.3 0.2 - - - -
63B ALA* 1.3 73.4 - - + +
65B ASP* 1.3 66.8 + - - +
67B THR* 3.3 8.4 + - + -
68B HIS* 3.1 40.5 + - + +
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Residues in contact with ASP 65 (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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239A VAL* 4.1 10.7 - - + +
243A LEU* 4.7 1.0 - - + +
246A ALA* 3.5 12.2 - - - +
247A TYR* 2.7 31.5 + - - -
248A PHE* 2.9 23.4 + - + -
249A ALA* 2.9 43.1 + - - +
250A PRO* 3.7 4.5 - - - +
61B GLY 3.1 17.8 + - - +
62B LYS* 3.6 4.9 - - - +
64B LEU* 1.3 76.5 - - - +
66B ILE* 1.3 61.3 + - - +
68B HIS* 3.1 18.9 + - - +
69B SER 3.5 0.2 + - - -
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE* 3.5 33.7 - - + -
34B GLY 3.5 25.1 - - - +
37B ALA* 3.7 16.4 - - + +
38B TYR* 3.8 16.2 - - + +
51B LEU* 4.5 4.7 - - + -
62B LYS* 2.8 29.4 + - + +
63B ALA 3.9 3.1 - - - +
65B ASP* 1.3 71.8 - - - +
67B THR* 1.3 62.8 + - - +
69B SER* 2.6 25.8 + - - +
70B MET* 3.4 25.0 + - + +
78B VAL* 4.0 18.2 - - + -
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A THR* 3.9 19.0 + - + +
178A GLN* 3.7 26.7 - - - +
63B ALA 2.7 27.9 + - - -
64B LEU* 3.5 13.5 - - + +
65B ASP 3.3 0.2 - - - -
66B ILE* 1.3 74.2 - - - +
68B HIS* 1.3 63.7 + - + +
70B MET* 3.1 26.1 + - + +
71B VAL 4.4 0.5 + - - -
76B SER 5.9 1.1 - - - +
77B LYS* 6.5 0.2 - - - -
78B VAL* 3.0 26.5 + - - +
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Residues in contact with HIS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 4.8 1.1 - - + -
170A SER* 3.7 11.6 - - - -
171A ARG* 3.5 49.4 + - + +
174A THR* 4.4 13.5 - - + -
175A PHE* 3.7 30.0 - + - -
235A ALA* 4.9 3.4 - - + -
238A GLU* 5.5 3.3 + - - -
239A VAL* 3.9 17.2 - - + +
249A ALA* 3.8 12.0 - - + +
64B LEU* 3.1 35.3 + - + +
65B ASP* 3.1 12.6 + - - +
67B THR* 1.3 78.9 - - + +
69B SER* 1.3 59.3 + - - +
70B MET 3.3 0.2 - - - -
71B VAL* 3.8 7.2 - - - +
72B MET* 3.7 13.4 - - + +
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Residues in contact with SER 69 (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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249A ALA* 3.8 23.5 - - - +
252A ALA* 4.0 5.8 - - - -
38B TYR* 3.9 7.4 - - - -
65B ASP 3.5 1.6 + - - -
66B ILE* 2.6 24.7 + - - -
68B HIS* 1.3 78.1 - - - +
70B MET* 1.3 76.4 + - - +
71B VAL 3.4 1.3 - - - -
72B MET* 3.0 21.2 + - - +
73B PHE* 3.1 32.5 + - - -
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Residues in contact with MET 70 (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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38B TYR 4.3 1.3 - - - +
41B GLY* 3.4 45.1 - - - +
42B LYS 3.8 4.0 - - - +
66B ILE* 3.4 22.7 - - + +
67B THR* 3.1 19.1 + - + +
69B SER* 1.3 101.7 + - - +
71B VAL* 1.3 62.1 + - - +
73B PHE* 3.1 17.1 + - + +
74B SER* 2.9 45.7 + - - +
76B SER* 3.5 22.2 - - - +
78B VAL* 4.6 5.8 - - + -
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Residues in contact with VAL 71 (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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170A SER* 3.6 35.7 - - - +
173A ARG* 3.8 24.3 + - + +
174A THR* 3.9 12.7 + - - +
184A ALA* 3.5 48.4 - - + +
185A SER* 3.7 11.5 + - - +
67B THR 4.4 1.2 + - - -
68B HIS 3.8 6.7 + - - +
70B MET* 1.3 77.6 - - - +
72B MET* 1.3 65.5 + - - +
73B GLY* 3.2 11.2 - - - +
74B SER 4.2 3.5 + - - -
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Residues in contact with MET 72 (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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166A VAL* 3.9 14.6 - - + +
167A LEU* 3.9 13.5 - - + -
170A SER* 3.3 35.9 - - - +
249A ALA* 3.4 27.8 - - + +
252A ALA* 3.6 11.2 - - + -
253A ALA* 3.4 32.1 - - + -
256A LYS* 3.5 41.0 + - + +
68B HIS 3.7 11.4 - - - +
69B SER* 3.0 11.4 + - - +
71B VAL* 1.3 78.8 - - - +
73B PHE* 1.3 61.9 + - + +
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Residues in contact with PHE 73 (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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39A ILE* 4.2 11.9 - - + -
43A ASP* 5.7 0.2 - - - -
252A ALA* 3.5 27.8 - - + -
255A VAL* 6.1 1.1 - - + -
256A LYS* 5.4 7.2 - - + +
38B TYR* 3.9 22.4 - + - -
42B LYS* 3.7 75.0 - - + +
69B SER* 3.1 36.5 + - - -
70B MET* 3.2 12.3 + - + +
72B MET* 1.3 78.8 - - + +
73B GLY* 1.3 62.1 - - - +
74B SER* 4.5 2.9 - - - +
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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
------------------------------------------------------------
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