Contacts of the strand formed by residues 41 - 50 (chain A) in PDB entry 5LAL
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 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PRO* 3.4 4.2 - - - +
40A CYS* 1.3 80.1 - - - +
42A HIS* 1.3 63.8 + - - +
43A PHE* 3.7 39.0 - - + -
127A HIS* 4.4 14.1 + - - -
155A PHE* 5.1 4.0 - - + -
181A ILE 3.7 1.1 - - - +
182A LYS* 3.6 2.8 - - - -
183A LEU* 2.9 53.2 + - + +
186A CYS* 4.0 7.2 - - - -
211A EDO 6.3 0.2 - - - -
37B LYS* 4.0 23.9 - - - +
38B LYS* 5.4 2.7 - - - +
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Residues in contact with HIS 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 LYS* 3.5 25.5 + - - +
39A PRO* 4.2 10.5 - - + +
41A LYS* 1.3 78.3 - - - +
43A PHE* 1.3 85.7 + - - +
44A SER* 4.9 3.9 - - - -
180A ASP* 3.7 25.1 + - - +
181A ILE 3.2 9.9 - - - -
182A LYS* 4.2 20.5 - - + +
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Residues in contact with PHE 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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41A LYS* 3.7 34.8 - - + -
42A HIS* 1.3 83.9 - - - +
44A SER* 1.3 59.8 + - - +
45A PHE* 3.8 31.9 - + + -
122A PHE* 3.9 10.5 - + - -
127A HIS* 3.8 16.6 - + - -
131A LEU* 4.5 4.0 - - + -
155A PHE* 3.5 40.8 - + - -
179A MET 4.4 0.4 - - - -
180A ASP* 3.3 3.6 - - - -
181A ILE* 2.8 49.9 + - + -
183A LEU* 5.4 1.3 - - + -
216A GLY* 3.7 22.7 - - - +
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Residues in contact with SER 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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42A HIS* 4.9 4.5 - - - -
43A PHE* 1.3 74.5 - - - +
45A PHE* 1.3 65.3 + - - +
46A TYR* 6.1 0.6 - - - -
88A MET* 3.7 19.8 - - - +
178A LYS* 3.0 22.3 + - - -
179A MET 3.4 4.9 - - - -
180A ASP* 2.8 24.5 + - - -
216A GLY* 5.8 0.4 + - - -
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Residues in contact with PHE 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 PHE* 3.8 23.1 - + + -
44A SER* 1.3 78.2 + - - +
46A TYR* 1.3 68.6 + - - +
86A ILE* 3.3 27.6 - - + -
87A THR 3.3 13.9 - - - +
88A MET* 4.0 11.0 - - - +
97A VAL* 4.1 7.0 - - + -
120A LEU* 4.0 19.5 - - + -
122A PHE* 4.2 13.7 - + - -
178A LYS* 3.5 4.6 - - - +
179A MET* 2.8 50.6 + - + +
181A ILE* 3.9 30.3 - - + -
216A GLY 3.8 20.0 - - - -
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Residues in contact with TYR 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 SER 6.1 0.2 - - - -
45A PHE* 1.3 77.8 - - - +
47A PHE* 1.3 60.3 + - - +
48A HIS* 3.8 8.1 - - + +
85A PRO 3.6 1.4 - - - +
86A ILE* 3.2 8.1 - - - -
87A THR* 2.9 37.3 + - - +
88A MET 3.6 19.7 - - - -
89A ASP* 3.3 29.4 - - - +
90A LYS* 3.3 35.5 - - + -
167A ASP* 4.0 13.0 - - + -
176A ARG* 4.0 22.7 - - + -
177A VAL 3.3 4.3 - - - +
178A LYS* 3.7 44.6 + - + +
210A EDO 4.2 1.8 + - - -
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Residues in contact with PHE 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 PHE 4.2 0.4 + - - -
46A TYR* 1.3 73.8 - - - +
48A HIS* 1.3 77.3 + - - +
49A ASP* 3.9 13.7 - - + -
82A PHE* 3.7 28.9 - + + -
84A GLY* 4.2 8.3 - - - -
85A PRO 3.6 6.1 - - - -
86A ILE* 3.8 8.7 - - + +
100A ALA* 3.7 30.7 - - + -
116A PHE* 4.4 13.0 - + - -
175A PHE* 3.8 32.5 - + - -
176A ARG* 3.2 6.8 - - - +
177A VAL* 2.8 40.8 + - + +
179A MET* 3.4 31.1 - - + +
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Residues in contact with HIS 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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46A TYR* 3.8 5.2 + - + +
47A PHE* 1.3 93.2 - - - +
49A ASP* 1.3 61.8 + - - +
50A ILE* 4.3 2.5 - - + -
61A THR* 3.8 5.1 + - + -
84A GLY* 3.9 0.5 - - - -
85A PRO* 3.3 39.4 + - + +
87A THR* 2.8 31.5 + - + -
90A LYS* 3.4 15.9 - - - -
91A ASN 3.7 0.4 - - - -
92A TYR* 3.3 44.9 - - + +
174A TYR* 2.7 30.4 + - + -
175A PHE 3.6 3.1 - - - -
176A ARG* 3.8 11.7 - - + +
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Residues in contact with ASP 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 PHE* 3.9 6.7 - - + -
48A HIS* 1.3 75.3 - - - +
50A ILE* 1.3 60.6 + - - +
51A LEU* 3.9 6.4 - - - +
61A THR* 3.5 2.4 + - - -
62A SER* 2.9 33.3 + - - -
82A PHE* 3.6 14.2 - - - +
104A TYR* 2.9 30.5 + - - -
173A LYS 3.9 0.2 - - - +
174A TYR* 3.2 9.4 - - - -
175A PHE* 3.0 60.9 + - + -
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Residues in contact with ILE 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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48A HIS* 5.5 1.1 - - + -
49A ASP* 1.3 75.1 - - - +
51A LEU* 1.3 63.5 + - - +
56A ASN* 4.1 11.7 - - - +
59A ASN* 3.6 30.3 - - - +
60A ALA* 3.3 6.8 - - - -
61A THR* 2.8 44.8 + - + +
62A SER* 3.3 6.2 + - - -
92A TYR* 3.8 34.8 - - + -
173A LYS 3.6 9.4 - - - +
174A TYR* 3.8 17.3 - - + -
1C NAG 3.7 31.2 - - - +
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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