Contacts of the strand formed by residues 177 - 185 (chain A) in PDB entry 5F1B
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 ALA 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A ASN* 3.7 27.8 - - - +
105A ALA* 4.1 10.3 - - + -
107A ASN 4.6 6.3 - - - +
108A CYS* 4.1 2.5 - - - -
109A TYR* 5.7 0.7 - - - -
132A PHE* 3.9 24.8 - - + +
160A PHE* 3.6 1.9 - - - -
161A LEU* 2.7 39.7 + - + +
176A PHE* 1.3 79.2 - - - +
178A GLU* 1.3 59.1 + - - +
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Residues in contact with GLU 178 (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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69A ASN* 3.4 9.4 + - - +
70A LEU* 2.9 40.4 + - + +
85A ARG* 2.7 39.3 + - - -
86A TRP* 2.8 27.1 + - - +
107A ASN 5.5 1.0 + - - -
109A TYR* 4.0 9.3 - - + -
154A HIS* 2.6 37.1 + - + +
158A ALA* 5.4 1.3 - - + -
159A PHE 3.5 5.4 - - - +
160A PHE* 4.7 1.6 - - + +
161A LEU* 4.4 0.7 - - - -
176A PHE* 4.4 13.5 - - + -
177A ALA* 1.3 75.2 - - - +
179A GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 179 (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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68A LEU 3.0 13.0 - - - -
70A LEU* 3.5 8.0 - - - +
158A ALA* 3.6 3.0 - - - +
159A PHE* 2.8 41.2 + - - +
161A LEU* 3.8 14.6 - - - +
177A ALA 3.8 0.8 + - - -
178A GLU* 1.3 76.4 - - - +
180A VAL* 1.3 68.5 + - - +
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Residues in contact with VAL 180 (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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66A VAL 3.7 0.2 - - - +
67A GLY* 3.4 3.3 - - - -
68A LEU* 2.7 39.9 + - + +
70A LEU* 3.6 19.5 - - + -
158A ALA* 4.3 5.4 - - + -
159A PHE* 4.4 6.1 - - + -
161A LEU* 4.5 0.6 - - - +
179A GLY* 1.3 79.6 - - - +
181A VAL* 1.3 63.7 + - - +
559B ARG* 5.0 2.0 - - - +
562B ALA* 3.5 26.6 - - + +
563B ASN* 4.1 5.2 - - + +
566B THR* 3.4 16.4 - - + +
1D NAG 3.3 36.1 - - + +
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Residues in contact with VAL 181 (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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65A SER* 4.4 7.0 - - - -
66A VAL 3.2 10.8 - - - +
67A GLY* 4.6 1.1 - - - -
97A VAL* 5.0 4.0 - - + -
98A ASN 4.8 2.5 - - - +
99A TYR* 4.4 15.5 - - + -
159A PHE* 4.6 9.6 - - + -
161A LEU* 4.6 5.4 - - + -
166A ALA* 4.2 24.9 - - + -
180A VAL* 1.3 82.7 - - - +
182A ALA* 1.3 70.5 + - - +
183A PHE* 3.9 26.2 - - + -
562B ALA* 3.5 15.1 - - - +
565B THR* 3.5 17.6 - - - +
566B THR* 5.1 1.1 + - - -
569B LEU* 4.1 15.3 - - + +
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Residues in contact with ALA 182 (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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64A ARG 4.1 0.3 - - - +
65A SER* 3.2 4.0 - - - -
66A VAL* 2.8 38.9 + - + +
68A LEU* 5.5 2.7 - - + -
181A VAL* 1.3 76.6 - - - +
183A PHE* 1.3 66.5 + - - +
184A LEU* 4.8 6.7 - - + -
558B LEU* 4.6 5.4 - - + +
561B LEU* 3.9 18.6 - - + -
562B ALA* 3.7 27.5 - - + +
565B THR* 4.4 3.1 - - - -
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Residues in contact with PHE 183 (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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33A ILE* 3.4 33.4 - - + -
34A PRO 4.2 6.4 + - - +
35A LEU* 3.3 18.3 - - + +
36A GLY 2.8 24.4 + - - -
64A ARG 3.5 2.5 - - - -
65A SER* 3.7 26.2 - - - -
97A VAL* 4.7 7.4 - - + -
98A ASN 5.1 1.3 - - - -
181A VAL* 3.9 17.7 - - + -
182A ALA* 1.3 73.5 - - - +
184A LEU* 1.3 65.1 + - - +
561B LEU* 4.1 2.0 - - - +
565B THR* 4.0 16.1 + - + -
569B LEU* 4.0 13.5 - - + -
584B ILE* 3.9 35.4 - - + -
585B LEU* 3.9 21.3 - - + -
588B LYS* 6.1 1.8 - - + -
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Residues in contact with LEU 184 (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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35A LEU* 4.0 2.1 - - - +
36A GLY* 3.3 12.3 - - - +
38A ILE* 5.2 8.5 - - + -
43A LEU* 4.7 4.0 - - + -
63A LEU* 3.4 9.4 - - - +
64A ARG* 2.7 38.9 + - + +
66A VAL* 3.8 27.4 - - + -
182A ALA* 4.8 3.1 - - + -
183A PHE* 1.3 77.9 - - - +
185A ILE* 1.3 65.5 + - - +
186A LEU* 4.0 23.8 - - + -
558B LEU* 3.6 37.2 - - + -
561B LEU* 3.7 24.2 - - + -
585B LEU* 4.8 0.5 - - - +
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Residues in contact with ILE 185 (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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35A LEU* 3.7 23.8 - - + -
36A GLY 2.7 13.7 + - - +
37A VAL* 4.7 16.0 - - + +
38A ILE* 3.4 28.3 + - - +
48A VAL* 5.8 0.2 - - + -
51A LEU* 3.6 31.6 - - + -
56A LYS 4.8 5.4 - - - +
57A LEU* 4.1 29.2 - - + -
62A GLN* 3.4 9.0 - - - +
63A LEU* 3.7 20.0 - - + -
184A LEU* 1.3 72.5 - - - +
186A LEU* 1.3 71.9 + - - +
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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
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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