Contacts of the strand formed by residues 37 - 52 (chain A) in PDB entry 5TIN
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 VAL 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ARG* 3.7 9.6 - - - +
30A PRO* 3.4 45.5 - - + +
31A ASN* 5.8 1.3 - - - +
35A PRO 3.7 0.4 + - - -
36A PRO* 1.3 71.3 - - - +
38A GLN* 1.3 61.1 + - - +
39A VAL* 3.6 19.9 + - + -
68A TRP* 4.0 20.4 - - + -
69A ASN 5.0 3.8 - - - +
94A TRP* 4.0 15.7 - - + -
165A ASP 3.0 8.3 + - - +
166A LEU* 3.7 10.7 - - + +
167A ILE* 2.9 28.9 + - - +
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Residues in contact with GLN 38 (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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36A PRO* 3.4 17.6 + - - +
37A VAL* 1.3 71.6 - - - +
39A VAL* 1.3 63.5 + - - +
40A THR* 4.1 3.0 + - - +
67A LYS 3.7 2.3 - - - +
68A TRP* 3.6 17.7 - - - +
69A ASN 4.7 1.6 + - - -
167A ILE* 3.5 36.2 - - - +
169A GLU* 4.2 11.4 - - - +
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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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37A VAL* 4.0 9.0 - - + -
38A GLN* 1.3 75.4 - - - +
40A THR* 1.3 70.6 + - - +
41A CYS* 4.1 14.6 - - - -
66A GLN* 4.1 23.6 - - + +
67A LYS 3.3 9.6 - - - +
68A TRP* 4.2 3.6 - - + -
96A PRO* 3.7 17.3 - - + -
166A LEU* 3.5 31.6 - - + -
167A ILE 2.8 8.5 + - - +
168A PHE* 3.8 15.0 - - + +
169A GLU* 3.0 29.3 + - - +
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Residues in contact with THR 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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38A GLN* 4.1 3.5 + - - +
39A VAL* 1.3 74.6 + - - +
41A CYS* 1.3 63.1 + - - +
42A ASN* 5.7 0.2 + - - -
65A ARG 3.7 0.7 - - - +
66A GLN* 3.4 3.8 - - - -
67A LYS* 2.8 48.6 + - + +
169A GLU* 3.3 8.8 + - - +
170A TRP 4.2 1.3 - - - +
171A GLN* 3.4 45.5 - - + +
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Residues in contact with CYS 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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39A VAL* 4.1 15.5 - - - -
40A THR* 1.3 79.7 - - - +
42A ASN* 1.3 62.4 + - - +
64A LEU* 5.0 2.2 - - + -
65A ARG 3.3 6.5 - - - +
66A GLN* 4.3 4.7 - - - -
98A LEU* 4.1 25.6 - - - -
156A LEU* 4.3 11.9 - - + -
168A PHE* 4.5 8.7 - - - -
169A GLU 2.9 14.5 + - - +
170A TRP* 3.4 10.7 - - + -
171A GLN* 3.0 23.3 + - - +
175A PRO* 4.4 0.2 - - - +
210A ILE* 4.2 21.3 - - + -
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Residues in contact with ASN 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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40A THR 5.7 0.8 + - - -
41A CYS* 1.3 75.4 - - - +
43A ILE* 1.3 64.1 + - - +
63A PHE 3.9 0.2 - - - +
64A LEU* 4.3 0.5 - - - +
65A ARG* 2.7 82.2 + - - +
67A LYS* 4.1 8.5 - - - +
170A TRP* 4.4 1.3 - - - -
171A GLN* 3.0 35.0 + - - +
175A PRO* 3.1 20.9 - - + +
177A GLN* 3.2 13.5 + - - +
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Residues in contact with ILE 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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42A ASN* 1.3 79.7 - - - +
44A PHE* 1.3 60.8 + - - +
45A ILE* 4.0 22.7 - - + -
62A ILE* 4.3 16.2 - - + -
63A PHE 3.3 6.5 - - - +
64A LEU* 4.0 21.1 - - + -
65A ARG* 4.2 0.4 - - - -
154A MET* 3.9 28.9 - - + -
156A LEU* 4.8 3.1 - - + -
170A TRP* 4.3 14.1 - - + -
175A PRO 2.9 7.7 + - - +
176A VAL* 3.5 28.7 - - + -
177A GLN* 2.9 32.6 + - - +
212A VAL* 4.6 4.5 - - + -
214A PHE* 4.5 3.8 - - + -
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Residues in contact with PHE 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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43A ILE* 1.3 74.5 - - - +
45A ILE* 1.3 59.9 + - - +
46A ASN* 3.4 35.7 + - + -
62A ILE* 3.2 6.6 - - - +
63A PHE* 2.9 56.2 + + + -
65A ARG* 3.7 25.9 - - - +
177A GLN* 3.5 24.5 - - + +
178A VAL 4.2 2.9 - - - -
179A ALA* 3.6 33.4 - - + -
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Residues in contact with ILE 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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43A ILE* 4.0 15.3 - - + -
44A PHE* 1.3 72.9 - - - +
46A ASN* 1.3 60.1 + - - +
47A SER 3.6 26.0 - - - +
48A PHE* 4.1 16.4 - - + -
60A VAL* 4.9 3.4 - - + -
61A ASN 3.9 3.4 - - - +
62A ILE* 4.3 7.9 - - + -
154A MET* 5.4 1.3 - - + -
176A VAL* 4.0 12.8 - - + -
177A GLN 2.8 15.8 + - - +
178A VAL* 4.3 13.9 - - + -
179A ALA* 3.0 26.3 + - - +
182A LEU* 4.1 13.2 - - + +
189A LEU* 5.7 0.7 - - + -
214A PHE* 3.5 39.5 - - + -
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Residues in contact with ASN 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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44A PHE* 3.4 26.3 + - + +
45A ILE* 1.3 74.5 - - - +
47A SER* 1.3 64.2 + - - +
61A ASN* 2.8 37.9 + - - +
62A ILE 4.7 0.4 - - - +
63A PHE* 4.7 15.2 - - + -
131A ARG* 4.0 14.3 - - - +
179A ALA* 4.3 11.2 - - - +
182A LEU* 4.7 5.5 - - - +
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Residues in contact with SER 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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45A ILE* 3.3 8.7 - - - +
46A ASN* 1.3 85.1 - - - +
48A PHE* 1.3 63.4 + - - +
49A GLY 5.2 0.2 + - - -
59A ARG* 5.2 1.2 + - - +
60A VAL* 3.3 5.0 - - - -
61A ASN* 3.0 44.3 + - - +
182A LEU* 4.3 10.8 - - - -
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Residues in contact with PHE 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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45A ILE* 4.1 13.9 - - + -
47A SER* 1.3 77.4 + - - +
49A GLY* 1.3 62.1 + - - +
51A ILE* 4.0 18.4 - - + -
58A TYR* 3.7 33.7 - + - -
59A ARG 3.5 5.6 - - - -
60A VAL* 3.7 13.5 - - + -
152A CYS* 5.2 0.4 - - + -
182A LEU* 4.0 24.8 - - + +
183A THR 4.8 1.7 - - - +
184A LEU* 3.7 34.3 - - + +
189A LEU* 4.4 13.9 - - + -
214A PHE* 4.0 37.7 - + + -
216A LEU* 4.2 17.9 - - + -
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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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47A SER* 5.2 0.8 + - - -
48A PHE* 1.3 79.2 - - - +
50A SER* 1.3 70.4 + - - -
51A ILE* 3.1 12.8 + - - +
58A TYR* 3.8 1.7 - - - +
59A ARG* 2.9 30.3 + - - -
184A LEU* 5.2 1.6 - - - -
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Residues in contact with SER 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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49A GLY* 1.3 72.9 - - - +
51A ILE* 1.3 59.6 + - - +
52A ALA* 3.1 13.1 + - - +
57A ASP* 3.5 9.0 - - - +
58A TYR* 3.6 4.7 - - - -
59A ARG* 3.3 46.7 + - - +
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Residues in contact with ILE 51 (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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48A PHE* 4.0 6.1 - - + -
49A GLY* 3.9 8.7 - - - +
50A SER* 1.3 75.4 - - - +
52A ALA* 1.3 58.0 + - - +
53A GLU* 4.0 10.9 - - - +
57A ASP 3.6 4.9 - - - +
58A TYR* 3.9 19.1 - - + -
140A MET* 3.8 23.6 - - + -
184A LEU* 3.5 33.0 - - + -
186A GLN* 4.6 11.8 + - - +
187A PHE* 3.6 38.3 - - + -
216A LEU* 3.9 20.9 - - + -
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Residues in contact with ALA 52 (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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50A SER 3.1 5.8 + - - +
51A ILE* 1.3 72.3 - - - +
53A GLU* 1.3 62.3 + - - +
54A THR* 4.3 9.0 - - - +
55A THR* 3.2 23.1 - - - +
56A MET* 2.9 21.8 + - - -
57A ASP* 2.9 24.6 + - - +
140A MET* 3.7 4.7 - - - +
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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