Contacts of the helix formed by residues 35 - 50 (chain A) in PDB entry 1SNG
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 SER 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A TRP* 1.3 78.4 - - - +
36A PRO* 1.3 66.6 - - - +
37A TYR* 3.4 4.9 + - - +
38A SER* 3.1 33.2 + - - -
39A VAL* 3.0 24.8 + - - +
162A LEU* 3.3 15.5 - - - +
301A HIS* 3.0 13.1 + - - -
303A ALA* 4.5 2.7 - - - -
353A LEU 2.6 21.8 + - - -
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Residues in contact with PRO 36 (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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12A HIS* 3.7 12.8 - - + +
15A PHE* 3.9 2.6 - - + -
16A ALA* 3.7 30.3 - - + -
34A TRP* 3.5 33.8 - - + +
35A SER* 1.3 83.7 - - - +
37A TYR* 1.3 55.5 + - - +
40A ALA* 2.9 35.0 + - - +
352A ILE* 3.3 35.4 - - + +
355A LEU* 3.8 14.4 - - + +
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Residues in contact with TYR 37 (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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12A HIS* 3.9 8.5 - - - -
35A SER* 3.1 7.4 - - - +
36A PRO* 1.3 75.8 - - - +
38A SER* 1.3 78.4 + - - +
40A ALA* 3.9 1.0 - - - +
41A CAF 3.0 70.2 + - + +
73A LEU* 3.2 47.0 + - + +
74A ASP* 4.9 0.5 - - - -
76A ALA* 4.2 8.3 - - + -
77A VAL* 3.1 38.0 - - + +
85A SER* 4.2 9.9 + - - -
109A PRO* 4.0 11.6 + - - +
162A LEU* 4.6 4.0 - - + -
351A ALA* 4.6 2.2 - - + -
352A ILE 2.9 17.8 + - - +
353A LEU* 3.8 16.4 - - + -
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER* 3.1 16.6 + - - -
37A TYR* 1.3 93.4 - - - +
39A VAL* 1.3 60.1 + - - +
41A CAF 3.6 3.6 - - - +
42A ALA* 3.0 29.6 + - - +
85A SER* 5.0 0.5 + - - -
160A ASN* 3.0 39.5 + - - +
161A ALA 4.6 0.2 + - - -
162A LEU* 3.7 13.7 - - - +
301A HIS* 3.5 13.0 - - - -
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Residues in contact with VAL 39 (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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15A PHE* 4.0 9.6 - - + -
19A LEU* 4.4 5.4 - - + -
34A TRP* 3.6 24.9 - - + -
35A SER 3.0 15.7 + - - +
38A SER* 1.3 74.2 - - - +
40A ALA* 1.3 60.3 + - - +
42A ALA* 3.3 5.5 + - + +
43A LEU* 2.9 51.6 + - + +
267A LEU* 3.7 33.4 - - + -
271A LEU* 5.1 0.9 - - + -
299A VAL* 6.0 2.2 - - + -
301A HIS* 4.0 17.9 - - + -
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Residues in contact with ALA 40 (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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12A HIS* 4.1 12.8 - - + +
15A PHE* 3.8 16.0 - - + -
36A PRO 2.9 20.8 + - - +
37A TYR 3.9 0.4 - - - +
39A VAL* 1.3 75.7 - - - +
41A CAF 1.3 53.5 + - - +
43A LEU* 3.4 1.4 + - - +
44A GLY* 2.8 32.6 + - - -
62A LEU* 4.1 22.2 - - + +
69A LEU* 4.5 4.8 - - + +
73A LEU* 3.8 19.1 - - + +
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Residues in contact with CAF 41 (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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37A TYR* 3.0 68.0 + - + +
38A SER* 3.6 3.4 - - - +
40A ALA* 1.3 75.3 + - - +
42A ALA* 1.3 73.6 + - - +
44A GLY 3.2 0.7 + - - -
45A VAL* 2.9 33.3 + - - +
70A LEU* 3.5 7.3 - - - +
73A LEU* 3.6 15.2 - - + +
74A ASP* 5.0 3.4 - - - -
85A SER* 4.2 8.3 - - - +
87A THR* 3.2 37.9 + - - +
105A MET* 4.8 1.2 - - - +
108A ARG* 3.7 32.8 - - - -
109A PRO 4.9 2.5 - - - +
111A SER* 3.6 19.4 + - - +
160A ASN* 4.0 10.5 - - - +
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Residues in contact with ALA 42 (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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38A SER 3.0 18.7 + - - +
39A VAL* 3.3 6.9 + - - +
41A CAF 1.3 86.9 + - - +
43A LEU* 1.3 59.4 + - + +
45A VAL* 3.4 5.5 + - - +
46A LEU* 3.0 34.2 + - + +
87A THR* 5.0 1.8 - - + -
158A LEU* 3.7 34.7 - - + +
160A ASN* 5.3 3.1 - - + +
299A VAL* 5.3 6.3 - - + -
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Residues in contact with LEU 43 (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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15A PHE* 4.2 10.5 - - + -
39A VAL* 2.9 42.6 + - + +
40A ALA 3.9 2.9 - - - +
42A ALA* 1.3 75.1 - - + +
44A GLY* 1.3 57.1 + - - +
46A LEU* 3.4 16.0 + - + +
47A ALA* 2.8 29.3 + - - +
58A LEU* 3.9 26.8 - - + +
61A LEU* 4.1 14.4 - - + -
62A LEU* 4.1 12.7 - - + +
271A LEU* 3.8 37.9 - - + -
276A VAL* 5.3 0.4 - - + -
279A LEU* 4.7 4.9 - - + -
299A VAL* 5.2 7.2 - - + -
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Residues in contact with GLY 44 (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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40A ALA 2.8 21.8 + - - -
41A CAF 3.2 1.5 + - - -
43A LEU* 1.3 70.5 - - - +
45A VAL* 1.3 59.2 + - - +
47A ALA* 3.2 3.3 + - - -
48A ALA* 2.9 24.4 + - - +
62A LEU* 3.9 14.3 - - - +
66A PRO* 3.2 20.6 - - - +
69A LEU* 5.2 1.8 - - - -
70A LEU* 4.0 12.5 - - - +
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Residues in contact with VAL 45 (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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41A CAF 2.9 24.1 + - - +
42A ALA* 3.7 6.3 - - - +
44A GLY* 1.3 73.7 - - - +
46A LEU* 1.3 66.8 + - + +
48A ALA* 3.2 15.5 + - - +
49A GLY 3.3 8.0 + - - -
70A LEU* 4.0 10.1 - - + +
101A PHE* 3.4 29.0 - - + -
104A THR* 4.3 11.0 - - + -
105A MET* 3.8 30.5 - - + -
108A ARG* 3.8 35.0 - - + -
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Residues in contact with LEU 46 (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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42A ALA* 3.0 22.9 + - + +
43A LEU* 3.8 10.1 - - + +
45A VAL* 1.3 76.6 - - + +
47A ALA* 1.3 58.5 + - - +
49A GLY* 3.1 4.9 + - - -
50A ALA* 3.0 27.9 + - - +
58A LEU* 4.2 10.3 - - + -
89A LEU* 4.6 7.2 - - + -
101A PHE* 4.5 10.5 - - + -
105A MET* 6.0 0.2 - - + -
158A LEU* 4.0 25.6 - - + -
279A LEU* 4.0 25.8 - - + -
286A LEU* 4.5 3.1 - - - +
289A ILE* 4.0 22.6 - - + +
296A VAL* 4.1 21.8 - - + -
299A VAL* 4.5 13.5 - - + -
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Residues in contact with ALA 47 (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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43A LEU 2.8 18.9 + - - +
44A GLY* 3.3 9.0 - - - +
45A VAL 3.2 0.2 - - - -
46A LEU* 1.3 76.8 - - - +
48A ALA* 1.3 60.3 + - - +
50A ALA* 3.2 11.8 + - - +
55A ARG* 2.9 25.5 + - + +
58A LEU* 3.8 28.2 - - + +
59A THR* 4.7 7.9 - - + -
62A LEU* 4.9 3.1 - - + -
66A PRO* 4.0 16.8 - - + -
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Residues in contact with ALA 48 (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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44A GLY 2.9 12.3 + - - +
45A VAL 3.2 10.7 + - - +
47A ALA* 1.3 76.7 - - - +
49A GLY* 1.3 57.8 + - - +
51A ARG* 3.1 18.5 + - - -
55A ARG* 3.8 10.2 + - - +
66A PRO* 3.9 11.6 - - + +
70A LEU* 5.0 2.2 - - + -
101A PHE* 5.2 1.3 - - + -
104A THR* 4.0 25.6 - - + +
288A GLY* 4.9 0.3 - - - -
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Residues in contact with GLY 49 (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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45A VAL 3.3 4.4 + - - -
46A LEU 3.1 8.4 + - - -
48A ALA* 1.3 77.2 - - - +
50A ALA* 1.3 57.4 + - - +
51A ARG* 3.7 2.7 - - - -
101A PHE* 4.1 7.3 - - - -
286A LEU* 3.3 12.5 - - - -
288A GLY* 2.8 36.1 + - - -
289A ILE* 3.4 21.5 + - - -
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Residues in contact with ALA 50 (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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46A LEU 3.0 14.8 + - - +
47A ALA* 3.2 16.5 + - - +
49A GLY* 1.3 77.9 - - - +
51A ARG* 1.3 80.1 + - - +
54A THR* 4.0 6.3 - - + -
55A ARG* 3.6 30.2 + - - +
58A LEU* 4.3 3.4 - - + -
285A ASP 3.4 11.0 - - - +
286A LEU* 3.9 11.0 - - + -
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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